Mr Bemba was one of six would-be candidates deemed ineligible following hours of deliberation.
The ex-rebel leader had a war crimes conviction overturned in June.
However, the commission said Mr Bemba was excluded because of his conviction by the International Criminal Court (ICC) for bribing witnesses.
Mr Bemba, who returned to the DR Congo at the start of August after 11 years spent in exile or prison, is currently appealing against the ICC conviction.