Dellavedova had a chance to win it at the buzzer in regulation but his runner bounced off the rim. He made sure to seal it at the free-throw line in OT.
Gonzaga's Kevin Pangos had a miserable night, finishing with seven points on 3-of-18 shooting. He was just 1 of 10 from 3-point range, two days after a 30-point night against Brigham Young.
Rob Jones added 18 points and nine rebounds for the Gaels.
The teams were meeting for the 12th time in four years in a rivalry that is perhaps the fiercest on the West Coast right now.
At least one player called it a "hate-hate" relationship before the game, with Gonzaga center Robert Sacre saying Monday's game was personal and a matter of pride.
It lived up to its billing.
There were 14 lead changes and nine ties.
Saint Mary's led by as many as eight points early in the second half, but Gonzaga hung tight, pulling within 63-62 on Pangos' only 3-pointer with 3:58 left.
The Gaels still led 68-63 with 31 seconds left, but Harris hit a driving layup with 15 seconds remaining, then sank the game-tying 3-pointer.
Both teams had chances to take command in overtime.
Jorden Page grabbed a key rebound, then sank two free throws to put the Gaels up 76-72. Sam Dower's layup cut it to two again, but Dellavedova was fouled breaking through Gonzaga's full-court press and converted the free throws for the final margin.
The teams had split their season series, with Gonzaga winning 73-59 on its home court last month and Saint Mary's coming out on top 83-62 in January.
On Monday, it was tight from the start.
The first half saw 11 lead changes and five ties, including 36-all at the break.
Dellavedova finally got going after starting 1 of 5. He hit a 3 and Jones followed with a driving layup to get Saint Mary's within 28-26, only to see the Bulldogs go on a 6-0 run to take a 34-26 lead with 4:32 left in the half, capped by Harris' driving layup.
Saint Mary's closed out the first half on a 10-2 run. Dellavedova hit a jumper and 3-pointer, Jones another driving layup and Beau Levesque a 3-pointer that tied the score at 36 with 47 seconds left.
Sacre finished with 17 points for Gonzaga while Dower added 14 off the bench.
Page added 16 for Saint Mary's and Brad Waldow had 13 and eight rebounds.
Storylines Two titles for Gaels
R Saint Mary's Matthew Dellavedova scores 22 points.
• The Gaels win WCC regular-season and tournament titles.
• Gonzaga's Kevin Pangos scores seven points on 3-of-18 shooting.