The win helps the Lancers keep pace near the top of the increasingly crowded PacWest standings, moving the team to 9-3-1 overall, 7-2 (21 points) in conference.
The second place Argonauts fall to 10-3-1, 7-2-1 (22 points).
"I'm extremely proud of the work we did to go on the road and get a win against a very good team," said head coach Ryan Jorden. "Seeing the guys work that hard even into overtime to get the result was fantastic."
After both keepers had kept a clean sheet for 98 minutes, Michael Salazar knocked home his second goal of the season to claim the victory.
Carlos Figueroa fired a shot that was blocked, but the Lancers managed to keep possession. Alex Anderson ended up with the ball and played a short pass in through the box to Salazar who made sure to finish it.
Salazar has scored in each of the Lancers' last two games.
After sitting out the last five games with an injury, CBU keeper Joey Pacheco recorded his fourth shutout of the season, tallying five saves in the win.
"To not concede a goal on the road and add to our shutout total is terrific," said Jorden, whose team has now held opponents scoreless six times this season. "Now it's time to focus our efforts on Saturday's game and work to get the same result."
The Lancers stay in the Bay Area, facing Dominican on Saturday.