The US rockers were joined by the rapper for their second-to-last encore as they performed his big hit '99 Problems' after stunning the crowd with a 25-strong set that included 'Alive', 'Better Man' and 'Jeremy'.
Pearl Jam ended their set with Neil Young's 'Rockin' in the Free World', bringing the two-day Philadelphia festival to an end.
Earlier in the day, Run Dmc took to the stage for the first time in more than a decade and performed a number of their greatest hits including 'It's Tricky' and 'It's Like That'.
The group - made up of Joseph 'Run' Simmons and Darryl 'DMC' McDaniels - paid tribute to their late band member, DJ Jason 'Jam Master Jay' Mizell - who was tragically killed in October 2002 - by playing under a banner that read: 'Jam Master Jay Forever'.
Run told the crowd: ''After his assassination ... we put a silence on the group.''