Halted at the quarters, David Beckham and the Galaxy now must focus on domestic competitions as TFC advances in the CCL.
The Galaxy, unbeaten at home through 2011 and heavily favored, posted a second straight loss in the Home Depot Center.
It could have ended differently. Early in the match, Mike Magee ran behind the high TFC backline and lobbed the advancing keeper. The goal was ruled out as offside, but replays indicated the officials whistled incorrectly.
Toronto capitalized. At the other end, Ryan Johnson rose above rookie defender Tommy Meyer to pad a header into the far netting.
LA equalized both the night's the aggregate score when TFC defender Ty Harden turned the ball into his own night. Had he meant it, the former Galaxy player would have been praised for a smart finish.
Midway through the second half, Nick Soolsma slotted home a Johnson cross for the winner. Despite peppering from the Galaxy attack, the Canadians held on to progress.
Attendance in the HDC was capped at 7,500 due to an agreement with California State University, Dominguez Hills, which owns the campus where the stadium is built.
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