Hutu extremists killed tens of thousands of Tutsis and other people in Gikongoro as part of a massacre of about 800,000 Tutsis and moderate Hutus in three months of ethnic violence in 1994.
Bishop Augustin Misago was held in prison for one year before being absolved and freed in June.
As is usual, no details of the papal audience at the Vatican were given.
But the bishop said beforehand he wanted to thank the Pope for the steadfast support he had provided during the case.
The church argued that the prosecution of the Hutu bishop was an effort to break its influence in Rwanda and welcomed the June verdict.
The bishop received strong support from the Vatican right from the start of his trial. He would have faced a death penalty had he been found guilty.
Conspiracy
Bishop Misago has been in Europe receiving treatment for heart problems and said he was anxious to return to his diocese at Gikongoro in southern Rwanda now that he was better.
Hutu extremists killed tens of thousands of Tutsis and other people in Gikongoro as part of a massacre of about 800,000 Tutsis and moderate Hutus in three months of ethnic violence in 1994.
Bishop Misago was charged with helping to plan Rwanda's genocide, but always maintained his innocence, saying he only attended high-level meetings during the genocide to appeal for calm.
He told the BBC last year that he was the victim of an elaborate political conspiracy, with the Rwandan Government spoiling for a fight with the Catholic Church.
He said he had repeatedly spoken out against extremism and violence, and had extended what protection he could to those most in danger.
Bishop Misago's defence lawyers maintained there was never any real case to answer.
But the Catholic Church has faced strong criticism from genocide survivors and human rights groups for staying silent during the slaughter and for its failure to apologise afterwards.