The couple, who got engaged last year while on holiday in South Africa, exchanged vows in Ojai, California, in front of guests including Ben Affleck, Matt Damon, Howard Stern, Emily Blunt and John Krasinski, reported People magazine.
The couple's invitations requested that guests make a charitable donation in lieu of wedding gifts.
A number of celebrities also attended their rehearsal dinner.
The 45-year-old host began dating Molly, 34, in October 2009, shortly after he split from comic star Sarah Silverman after a five-year romance.
"After Jimmy and Sarah Silverman broke up, Molly and Jimmy both found themselves single, and they clicked. They're really happy together," a source said.