After the first seven penalty-takers scored, Panathinaikos' Antonios Petropoulas shot wide, allowing Bonera to clinch the game 5-3 in the shootout.
Panathinaikos dominated the match, but Djibril Cisse had a first-half goal disallowed after being called offside.
Panathinaikos also lost what appeared to be a legitimate goal in the 55th minute when Sidney Govou's shot off the crossbar crossed the line before being cleared by Bonera. The referee did not give the goal.
The game, which drew an announced crowd of 30,514 at the Pontiac Silverdome, was played on a temporary grass field like the one used for the 1994 World Cup.
American defender Oguchi Onyewu did not play for Milan while continuing to recover from a knee injury that cost him most of last season and limited him in this summer's World Cup.
