The Canadian side sit seventh in the Eastern Conference after their triumph, which ended a run of six winless matches.
Despite star striker Jermain Defoe being sidelined with a groin injury – the former Tottenham man is expected to arrive back from England on Monday – Toronto caused consistent problems in attack for their opponents.
Brazilian winger Jackson Goncalves gave them a 23rd-minute lead, netting a deflected strike after Gilberto's backheel played him in.
And England forward Luke Moore doubled Toronto's advantage on the stroke of half-time.
Michael Bradley's corner was headed back across the face of goal by Nick Hagglund and Moore was on hand to score a volley from close range.
Gilberto sealed Toronto's win with 36 minutes remaining with a tap-in before Jackson and Chivas USA's Nigel Reo-Coker both saw red for a clash.
The incident did not take the gloss off Toronto's win, though, as they recorded a much-needed victory.
Chivas USA remain rooted to the bottom of the Western Conference and are winless in their last 11 matches – of which 10 have been defeats.