Jonathan received medical treatment on Thursday while on a visit to London, his office said, describing it as "precautionary" and saying his condition was not serious.
Jonathan, who turned 56 on Wednesday, was due to be at an investment meeting in London on Thursday but was not well enough to attend. He has no known serious illnesses.
"President Jonathan has since been examined by competent medical practitioners. He has been advised to rest for a few days," the presidency said in a statement.
"The Presidency wishes to assure all Nigerians that President Jonathan's condition is nothing serious and that the medical attention he has sought is only precautionary."
Jonathan, a Christian from the southern oil-producing Niger Delta, came to power in May 2010 when former President Umaru Yar'Adua died after a long-running heart condition.
Jonathan won an election in 2011 and could be the ruling party candidate again when Africa's top oil producer and second largest economy goes to the polls in early 2015.