Gordon struck in the fifth minute of additional time on Tuesday to square the tie ahead of the second leg in Mexico, although Toluca have the slight advantage with an away goal up their sleeve.
The visitors to Buck Shaw Stadium in California took the lead in stunning fashion, when tournament-leading goal-scorer Raul Nava lashed home a vicious volley in the 67th minute.
Nava's seventh goal of the Champions League campaign was a pearler, as he took the remnants of a failed clearance from San Jose defender Jason Hernandez and turned it into a lead for the Liga MX side.
Hernandez lunged at a through ball from Toluca defender Aaron Galindo but his clearance effort just looped up into the air, and Nava pounced - taking the ball on the volley and dispatching it into the left side of the net from the edge of the area.
Nava also became Toluca's all-time highest scorer in the continental competition with 10 goals, heading Hector Mancilla (nine).
San Jose did not relent, though, and they gained some valuable momentum to take to the second leg next Wednesday - with coach Mark Watson making the vital change.
Gordon and Jeffrey Koval came on in the 73rd minute, in a double substitution for Hernandez and Sam Cronin - and the former paid dividends at the death.
Gordon rose highest from a Shea Salinas free-kick in the penultimate minute of the match, burying his header into the bottom left corner much to the delight of the home fans.
The Earthquakes are looking to reach the semi-finals for the first time, in their third visit to the last eight.
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