Jonathan made the allegations in a new book out on Friday called "Against The Run of Play", which documents how he became the first Nigerian incumbent head of state to lose an election.
He said Obama and his officials "made it very clear to me by their actions that they wanted a change of government in Nigeria and were ready to do anything to achieve that purpose".
"They even brought some naval ships into the Gulf of Guinea in the days preceding the election," he was quoted as saying in the 204-page book, by journalist Olusegun Adeniyi.
Jonathan won widespread praise for conceding to Buhari before the final results were announced, preventing deadly violence that blighted previous elections in Africa's most populous nation.
But he alleged Obama influenced Britain's former prime minister David Cameron and the current French president Francois Hollande to work against him.
"I got on well with... Cameron but at some point, I noticed that the Americans were putting pressure on him and he had to join them against me," he said.
"But I didn't realise how far President Obama was prepared to go to remove me until France caved in to the pressure from America."
Jonathan said he had a good relationship with Hollande, who was his first point of contact whenever there were difficulties with neighbouring Cameroon over the Boko Haram insurgency.
In the wake of the 2014 kidnapping of more than 200 schoolgirls from the northeast Nigerian town of Chibok, Hollande organised a security summit in Paris involving Nigeria and its neighbours.
The talks were instrumental in the creation of a regional fighting force, which has been key to weakening the Islamic State group affiliate.
"But weeks to the election, he had also joined the Americans in supporting the opposition against me," he added, according to an advance copy of the book seen by AFP.
Jonathan attributed opposition to his re-election to claims by Buhari's All Progressives Congress (APC) party that he was not doing enough to fight corruption.
"That was the same thing I kept hearing from the Americans without specific allegations," he added, rejecting claims he had done nothing to tackle the problem.
Buhari has accused Jonathan and his Peoples Democratic Party (PDP) of leaving his government with a "virtually empty" treasury and said "mind-boggling" amounts of public money were stolen.
Many senior figures in the PDP and Jonathan's administration, as well as his family members, are currently facing trial for corruption.
Buhari, who led a military government in the 1980s, has been successful in operations against Boko Haram, whose insurgency has left at least 20,000 people dead in Nigeria alone.
Jonathan, whose administration was accused of failing to properly equip and support the military against Boko Haram, again claimed Obama's administration undermined Nigeria's response.
Nigeria's ambassador to Washington in 2014 publicly criticised the United States for refusing to sell it attack helicopters on human rights grounds.
Jonathan said US laws prohibiting arms sales to countries with poor rights records "made the war against Boko Haram very difficult".
A US embassy official in Abuja said in a statement it was "surprising" Jonathan appeared to be reconsidering his view of the election.
Washington's policy before the vote was for a free, fair and transparent process, he said, adding the United States believed the result was "an expression of the will of the Nigerian people".
Britain echoed the view, and called the vote "a credit to the Nigerian people and a truly historic moment for Nigerian democracy".
It pointed to the assessment of independent observers, including the European Union, that there was "no evidence of systemic manipulation of the process".
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)