Montreal Impact had looked set to claim a critical victory in front of a sell-out crowd at the Estadio Azteca, after Ignacio Piatti had given the visitors a first half lead.
But in the second-last minute of regulation time, Peralta rose highest to head a free-kick past Montreal goalkeeper Evan Bush from just six yards.
Peralta's goal leaves the continental decider delicately poised heading into next week's second leg in Montreal.
Frank Klopas' Montreal entered the match having not won in four games in all competitions but struck a vital early blow in Mexico City, as Piatti opened the scoring in the 16th minute.
Dominic Oduro was afforded some space outside the box and his pass was allowed to run by Dilly Duka, before Piatti stepped in front of his marker and turned the ball inside the far post.
America were lucky Osvaldo Martinez was not sent off on the cusp of half-time as he tugged Oduro back, with the Montreal forward clear bearing down on goal.
But America's dominance - they finished the match with 28 shots to four - eventually led to a deserved equaliser, with half-time substitute Peralta breaking the Impact's resistance.
Bush was immense for the visitors as he made eight saves and claimed numerous high balls in his penalty area, but he could not keep a clean sheet.
The Impact are the first Canadian club to reach the Champions League final, while they are looking to become the first MLS outfit to win CONCACAF's premier continental title since Los Angeles Galaxy in 2000 - during the Champions Cup era.
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