Baldwin, 54, and Thomas, 28, exchanged "I do's" at St. Patrick's Old Cathedral in front of guests including Baldwin's brothers Stephen and Billy Baldwin, Tina Fey, Woody Allen, Mariska Hargitay, Robert Kennedy Jr. and Saturday Night Live executive producer Lorne Michaels.
Thomas, a yoga instructor, wore a silk magnolia Amsale gown with cap sleeves and a keyhole back neckline. Baldwin sported a tuxedo by Tom Ford. His daughter, 16-year-old Ireland, also wore Amsale. The reception took place in NYU's Kimmel Center.
Baldwin tweeted a picture of a wedding band on his left ring finger late Saturday.
Baldwin and Thomas became engaged three months ago after dating since last summer. Baldwin was previously married to Kim Basinger from 1993 to 2002.