Keshi, who steered the Super Eagles to Africa Cup of Nations glory in 2013 and the knock-out stage of this year’s World Cup finals, was sacked on October 16 after a string of poor performances.
But several senior officials at the Nigeria Football Federation (NFF) have revealed that Jonathan had ordered Keshi be reinstated and given a contract.
Should that happen, he would be on the bench for Nigeria’s next Africa Cup of Nations qualifiers against Congo and South Africa in November.
Keshi, who was in talks on Thursday with sports minister Tammy Danagogo, said he was unaware of any presidential intervention.
But he added: “If the president of my country asked me to return, who am I to refuse?”
The 52-year-old coach had earlier refused to comment on speculation that he could be reinstated, with a power struggle for leadership of the NFF rumbling on.
New NFF boss Amaju Pinnick sacked Keshi and his coaching staff soon after his appointment last month, adding that the hunt was on for a foreign coach.
Jonathan is said to have met Pinnick and Chris Giwa, who briefly led the NFF in August, at the presidential villa in the capital, Abuja, on Wednesday night.
“Keshi is back as Nigeria coach and he will be the one to lead the Super Eagles against Congo and South Africa next month,” said one senior official.
In a separate NFF statement released on Thursday, caretaker coach Shuaibu Amodu said Keshi should be allowed to take charge for the last two AFCON qualifiers.
He said the executive committee should reconsider as he did not have enough time to prepare for the games.
“The timeframe is too short to start tinkering with the fabric of the team or attempt to build a new team altogether,” he wrote in an open letter to NFF bosses.
Nigeria play Congo-Brazzaville in Pointe Noire on November 15 and South Africa in Uyo, southeast Nigeria, four days later.
They need to not only win both matches but beat Congo by a margin of two away goals to stand any chance of automatic qualification for the finals in Morocco next year.