Jim Cantamessa's 3-pointer with 5 minutes left put Siena in front 65-53. Scott Knapp's 3 restored the double-digit lead with 3 minutes left and the second-seeded Saints padded the lead over the scrappy No. 5 seed with free throws down the stretch.
Knapp hit 4-for-6 from 3-point range, finishing with 14 points. Cantamessa and Melvin Freeny added 13 each for the Saints.
Jamar Hunter scored 22 for St. Peter's, Kamaal McQueen had 19 and Ricky Bellinger 12.
Siena's only previous NCAA tournament appearance was in 1989 when the Saints beat Stanford 80-78 and lost to Minnesota 80-67. St. Peter's made the NCAA tournament twice, in 1991 and 1995, and failed to win a game either time.
McQueen tied the game at 35 early in the second half with a three-point play, and Kalief Allen put the Peacocks ahead with a pair of free throws.
Siena, the third-highest scoring Division I team in the nation behind Duke and Texas Christian with 87.7 points per game, took a 41-39 lead on a 3 by Cantamessa. After a three-point play by Hunter tied the game at 44, Siena surged back in front.
Cantamessa canned a 3 for a 49-44 lead with 11:24 to play, and Knapp hit his third 3 for a 58-51 advantage.
St. Peter's opened an early narrow lead and held it through most of the first half. Siena sputtered through a cold spell that saw the Saints miss their first eight 3-pointers and finish the half shooting 2-for-9 from behind the arc. They wound up 7-for-22.
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