The two-game series was level 2-2 on aggregate, so the Impact claimed the crown on the away goals tiebreaker. The Major League Soccer rivals played to a 0-0 draw in the first leg at Montreal.
With the win, the Impact earn a berth in the CONCACAF Champions League starting in August, which determines qualifiers for the 2014 Club World Cup.
Felipe also scored for the Impact, who trailed 1-0 after the first half.
Camilo and second-half substitute Daigo Kobayashi scored for the Whitecaps. Vancouver finished second in the national final for the fifth straight year.