Chris Wondolowski opened the scoring for the Quakes in the 18th minute before Corey Hertzog levelled just after the hour-mark.
The goal came in about in bizarre fashion as two San Jose players, forward Alan Gordon and defender Victor Bernardez, were off the pitch changing their boots at the time it occurred.
The laws of the game forced the two to remain on the sidelines until there was a stoppage but Hertzog managed to draw the Whitecaps level, taking full advantage of having two extra men which forced the Quakes to drop three valuable points and instead add just one to their pre-game tally of seven.
"It was really poor on our behalf of not realizing that the rule is you can't go back on the field [during the run of play]," Yallop said.
"There has to be a stoppage in play. It's just one of those nights that frustrates the team and frustrates me as a head coach."
Gordon also admitted it was a massive oversight: "It was really disappointing. I thought we had a great performance tonight and that's what's going to stick out. We lost a few points there because .it was a mistake.
"I take full responsibility for that. I feel like I let the team down, left them without two guys. They took advantage of it and we got punished."