The Pearl Jam frontman played four songs on a mandolin for the U.S. President and 85 Vip guests, who each paid $20,000 (£12,500) to attend the dinner in Tampa.
Vedder, who covered Neil Young's Rockin' in the Free World in his short set, joked, "I can't say I've ever played that many songs in a suit before."
He also voiced his support for Democratic candidate Obama as he told how, as an unemployed young man, he signed up for a government-funded training program that eventually helped him land a job working as a security supervisor.
He said, "I'm an example of someone who never made it to university. I did have this dream to be a musician. I felt that this dream had an expiration date... It was that job which allowed me to keep affording to (buy) guitars and microphones. For me, it all began with that ability to get the proper training for a decent job."
Vedder introduced the President, who in turn said thanks "for that unbelievable performance but more importantly for that story".
He added, "For you to share that story with us, Eddie, speaks volumes not only about you but about this country. That story captures better than anything what this campaign is about and what this country is about."
Obama is running for four more years in the White House and will go up against Republican pick Mitt Romney in the November (12) elections.