While the Indians didn't score on their next possession, Burroughs' senior guard Pedro Gonzales helped shave the deficit to four when he stole a pass from Major and led a fastbreak that resulted in a layup from Lawrence White with 1:16 left.
Maranatha then committed a back-court violation on its next offensive series.
However, the Indians didn't capitalize when a turnover on their side of the court led to a four-foot basket from Minutemen forward Andrew Elffers that put Maranatha up, 72-66, with 22.2 seconds left and sealed the game.
"We just made too many mistakes to win this game," said Indians Coach Adam Hochberg, whose team has already matched its win total (3-24) of last season. "But we did really well in this tournament and this will be a big confidence boost for us."
The Minutemen held a slight 36-35 advantage at the end of the first half.
Maranatha took its first lead at the 1:12 mark in the second quarter on two free throws from Darien McGee, who was fouled by Burroughs' Brandon Jimenez.
The Indians quickly seized the lead back on a three-pointer from Bennett, a Burbank transfer.
While Maranatha scored on a two-footer from Michael DeMeester, Bennett hit another three-pointer, assisted by White, with 45 seconds remaining to put Burroughs up, 35-33.
The Minutemen scored last, however, after a contested carry-over call gave last possession to Maranatha, which took the lead with a three-pointer from Major as time expired.