Jonathan's Peoples Democratic Party (PDP) is racked by in-fighting and has suffered a wave of defections to the main opposition group in recent months.
While he has not yet announced his candidacy for the vote next February, analysts say Jonathan is trying to rework the PDP to forge a party united behind him ahead of the election.
Chief government spokesman Labaran Maku said "those who were asked to go by the president" were aviation minister Stella Oduah; police affairs minister Caleb Olukolade; junior finance minister Yerima Ngama; and Godsday Orubebe, minister for the oil-producing Niger Delta region.
In October, she was accused of purchasing with public money two armoured vehicles at an inflated cost of USD 1.4 million (1.03 million euros).
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The allegations were probed by the presidency and parliament and made Oduah a target of intense media scrutiny.
Maku said Jonathan believed all four ministers had done a "great job" and had asked them "to step out" so they could pursue other interests.
"There is no significance (to the sackings) other than preparation for 2015," political analyst Clement Nwankwo told AFP.
Oduah played a key role in the president's 2011 election bid.
The latest departures come after Jonathan dismissed his chief of staff, Mike Oghiadomhe, on Monday.
Nigeria's media were split on whether the senior aide was pushed out because he had made too many enemies in the PDP or whether Jonathan wanted him committed full-time to the looming campaign.
The president also replaced the unpopular PDP chairman Bamanga Tukur in January, just days after removing the country's entire military top brass heading the fight against Islamist militants Boko Haram.
The president, a Christian from the south, has said it is too soon to discuss his political future.