Massapequa native Baldwin, 54, and his yoga instructor Thomas, 28, married at St. Patrick's Old Cathedral in a Catholic ceremony performed by the Rev. George Deas.
Thomas wore a silk magnolia Amsale gown with cap sleeves and a keyhole back neckline accented with crystal buttons. Baldwin's suit was designed by Tom Ford.
The two began dating last year and became in engaged in April. Baldwin was previously married to actress Kim Basinger; they have a daughter, Ireland, who attended the wedding Saturday in a slate silk chiffon gown also designed by Amsale.
The reception was being held at New York University's Kimmel Center.
The "Rock of Ages" actor warmly received congratulations from well-wishing fans on his way in for the service, said his friend and publicist, Matthew Hiltzik.
Hours before the ceremony, Baldwin tweeted lines from an Emily Dickinson poem. One read: "Was bridal e'er like this? A paradise, the host, And cherubim and seraphim The most familiar guest."
The wedding came about a week after Baldwin and a news photographer got into a scuffle outside of a courthouse where the actor was believed to have been picking up a marriage license. Baldwin and the photographer traded barbs over who shoved whom; no arrests were made.