The California side were rooted to the bottom of the Western Conference ahead of their home clash with the Seattle Sounders on Saturday and fell behind 2-0 and 3-1 to the Concacaf Champions League finalists.
But a Cristian Espinoza penalty in the 94th minute - completing the Argentine's hat-trick - sealed a dramatic 4-3 win, lifting them above the Vancouver Whitecaps in the West. In turn, the Quakes have received a huge boost in confidence.
"We had some bad weeks, but even in those bad weeks, everybody was positive," midfielder Jamiro Monteiro told reporters.
"We knew there would come a moment when we’d win a game and I think this will give us a lot of confidence for our next games. So, it did us good to win our home game and I hope now that we continue like this.”
Things don't get any easier for the Quakes, who travel to MLS Cup champions and CCL semi-finalists NYCFC this weekend.
The Cityzens have struggled themselves at the start of the new campaign, but picked up 5-4 and 6-0 wins over Toronto FC and Real Salt Lake, respectively, in their last two games. Quakes interim boss Alex Covelo is under no illusions about the challenge ahead.
“I don’t think it’s a secret that New York City FC and Seattle Sounders FC are very good teams," he said. "That’s why they were fighting for the Concacaf [Champions League] Final. We have a big game to play on Sunday, and we will try to address it tactically as best as we can.”
On preparing to play the reigning champs, Covelo added: "What we have tried to do is analyze New York City and tried to coach different things, not only in the attack but also in defense. We need to start step by step and work on different tactical situations that we need to address in relation to the game and in relation to the team that has to grow.”