Nigeria's third most powerful man has become the latest scalp in Olusegun Obasanjo's war against corruption.
Mr Wabara denies accepting money to push through an inflated budget
Senate Speaker Adolphus Wabara resigned two weeks after Mr Obasanjo accused him of taking a $400,000 bribe from the education minister.
The minister, Fabian Osuji, lost his job in March over the alleged bribe, which both he and Mr Wabara deny.
Mr Obasanjo has warned officials their greed is undermining his attempts to win international debt relief.
Nigeria remains one of the world's most corrupt countries.
On Monday, the housing minister was sacked and the former police chief was charged in court with graft.
Mr Wabara told a meeting of the Senate he would make himself available to investigators.
"It is my wish to voluntarily step aside as president of the senate to preserve the sanctity of that office," he said.
Two weeks ago in a television address, Mr Obasanjo accused the education minister of paying Mr Wabara more than $400,000 (£212,000) to ease through the passage of an education budget.
Six other MPs and officials are also being investigated by Nigeria's anti-graft agency - the EFCC.
Senator Ken Nnamani of Enugu State in southeastern Nigeria has been elected as the new speaker - beating Mr Obasanjo's favoured candidate in a vote, according to AFP news agency.