Air Force Capt. Jon Wu and Stephanie Hull tied the knot in a sunrise ceremony on the 86st floor observatory of the landmark building.
They were among 14 couples from eight states who were poised to say "I do" as part of a nationwide contest hosted by TheKnot.com.
Hull, who wore a strapless, creamy white gown with a long train, said she was "on cloud nine."
Their prize includes a honeymoon in the Bahamas.
Wu proposed to Hull last year by spelling out "will you marry me" in Christmas lights on a lawn outside their apartment building.
The ceremonies for the other winners were held on the 61st floor in a room decked out with floral arrangements and white chairs and with full views of the Big Apple.
The second couple to walk down the aisle were Sarah Marie Carpino and George Callahan, two firefighters from Lindenhurst, N.Y., who met on the job. Among those attending their ceremony was their "miracle baby," 17-month-old son, Jack, dressed in a little dark suit similar to his father's. Callahan held his son during the ceremony.
Doctors had told the couple that because Callahan had been diagnosed with testicular cancer they had one in a million chance of having children, said Carpino, wearing a white strapless gown.
They said they planned to pose for pictures outside their Long Island firehouse.