The meeting, according to findings, was to deliberate on the preparations for the governorship elections in both states.
The duo met with Jonathan for about one hour.
Fayose, who spoke with State House correspondents, said the Sunday bloody incident in Ado Ekiti was discused.
He accused the supporters of the All Progressives Congress (APC) for accosting some of his supporters who were returning from his campaign office and killed one of them.
According to him, the APC supporters hatched a plan to remove his branded T-shirt on his supporter that was killed, and replaced it with APC uniform to give an impression that the APC supporters were attacked by PDP supporters.
"What happened on Sunday was that APC supporters went about sweeping the feet of the president, who on Saturday led PDP bigwigs to a mega rally in Ado-Ekiti. I don't even have any objection to that because that is part of politics.
"There are some of my supporters who always sleep over in my campaign office. These people wearing my branded green T-shirts were returning home and the APC people accosted them.
"They macheted some of my supporters and even killed one of them. They were at the point of removing the deceased's branded T-shirt and replacing it with APC shirt when the OC MOPOL arrived the scene.
"As he was trying to stop them, Fayemi drove in to block him. It was when they wanted to mob the police officer that he shot tear gas into the air," Fayose averred.
He noted that his supporters were not deterred by the attack, and are fully mobilised to vote for him in the governorship election.
However, a socio-political group in the state, the Ekiti Parapo Development Association, has condemned the violence allegedly masterminded by leaders and supporters of the APC in the state at the weekend, which left one person dead and several others injured.
The group in a statement by its National Publicity Secretary, Ojo Ilesanmi, said based on the accounts of the incident, it was clear that the symbolic sweeping away of the foot prints of the members of the PDP and the supporters of the PDP governorship candidate, Fayose, including those of President Jonathan, who had converged on the state capital, Ado-Ekiti for the PDP grand rally led to the outbreak of the unfortunate and avoidable violence.
The group said it viewed the action of the APC in the state as a mark of provocation and disrespect for the office and person of the president and the number one citizen of the country.
“We note that in other climes, the office of the president of a country is accorded the utmost regard and respect, irrespective of political affiliation and differences."
Meanwhile, the national leader of the APC, Senate Bola Tinubu, has condemned in the strongest terms the attack by the police on APC members during a peaceful procession and campaign in Ekiti last Sunday.
According to him, the unprovoked attack on innocent citizens simply because they belong to another party was the height of political intolerance and heightens the doubts most Nigerians have about the ability of this government to guarantee free and fair elections in Ekiti, Osun and come 2015.
"The open boasts and direct threats by the ruling party to "capture" or win Ekiti back at all costs is beginning to manifest. The impunity of the police officers in Ekiti and glaring partisanship is clearly endorsed by the power that be. We this instance, we will demand for justice and enforcement of our fundamental human rights. I am fully with Governor Kayode Fayemi and the people of Ekiti State in confronting this rising tyranny and defeating barbaric tendencies."
Tinubu declared that he equally joins many well meaning Nigerians who demand and want peace to put the international community on notice that the present government is too desperate to be trusted to protect the fundamental rights of Nigerians and to conduct free and fair elections. Nigerians are confronted with a government that sanctions impunity while laying false claims to being democratic.
But the governorship candidate of the Labour Party (LP)) in Ekiti State, Hon. Opeyemi Bamidele, has cautioned Ekiti State chapter of All Progressives Congress (APC) not to play politics with the death of one Taiwo Akinola, a young man who was killed during a political fracas on Sunday in Ado-Ekiti.
Bamidele described as unfortunate a situation where APC in Ekiti would act in a manner as if the slain youth was its card-carrying member until he met his death, thereby pretending to be on the defensive.
He said the body language of APC leaders and that of Governor Kayode Fayemi in the last 72 hours indicated that they were playing into gallery, trying to look innocent when they are guilty.
A statement signed by Bamidele’s media aide, Hammed Salami, said: "We are amused by recent horse trading trailing the death Taiwo Akinola who was killed in Ado-Ekiti on Sunday morning by the ruling APC in Ekiti.
"Part of APC's attempts to pull the wool over the eyes of Ekiti people in this tragedy was the dramatic covering of Akinola's corpse with a APC branded vest at a time when a first aid support could have been offered him.
“All these were APC's desperate bid to cry wolf where there is none and make the guilty looks innocent. This ‘re-branding’ of corpse was done by APC goons in less than ten minutes after the victim gave up the ghost.
"I see this as height of ruthless politics and disrespect for the spirit of the departed youth. Just like every Ekiti indigene, we are pained by these lapses of the incumbent and call on APC to henceforth desist from its ignoble acts.
It is also of great concern that in less than 24 hours after the murder, the state governor raised a delegation of APC leaders and ranking cabinet members to pay a visit to the monarch of Odo-Owa Ekiti in Ijero Local Government Area where the victim hails from.
The political agenda behind this was to allow APC enjoy some level of public sympathy as if one of its members from the town had been killed by the thugs loyal to other political parties."
Meanwhile, the Ekiti State Council of Traditional Rulers has called on the Inspector General of Police (IG), Alhaji Mohammed Abubakar to effect the immediate removal of the Commander of Mobile Police Force in Ekiti, Mr Gabriel Serenkele.
In a statement signed by its Chairman and the Onitaji of Itaji, Oba Adamo Babalola, expressed displeasure over the killing of one Taiwo Akinola, a native of Odo-Owa Ekiti in Ijero Local Government on Sunday during a clash between the police and members of APC.
The monarchs said the incident, which happened barely 24 hours the President Jonathan visited the state, is totally sad and unacceptable to the generality of the people.
They said: “In all civilized nations, police are meant to maintain peace and protect the citizens. The barbaric act exhibited on Sunday by a member of the Nigeria Police Force gunning down an innocent citizen is totally unwarranted and unacceptable to the Council of Obas in Ekiti State. It is condemnable entirely.
“We want such a policeman to be removed from Ekiti State and incarcerated. He is not fit to participate in the coming election Ekiti people will react if such ugly occurrence rears its ugly head again.
“The Commissioner of Police should desist from giving life ammunition to some classes of police officers while checking peaceful demonstrations. He should not allow the security of the State to get out of hands.
“We don’t want Ekiti to be turned into a theatre of war as being preached in Abuja,” he said, appealing to all politicians to embrace peace for the coming election to be peaceful and acceptable to all parties.