The Major League Soccer squad remains in second place in Group 1, but moved within three points of Santos Laguna. The two sides meet October 24 in Torreon, Mexico, in a match that will determine the group winner and knockout round berth from the group.
If Toronto is to advance, it will need to beat Santos Laguna by at least two goals.
Despite virtually no angle, Amarikwa put the visitors in front in the 16th minutes, getting his downward header from Ryan Johnson's deep cross just inside the near post for his second Champions League goal.
Both players also were instrumental in Toronto FC's second goal as Dunfield disrupted Aguila's attempted buildup out of the back. Amarikwa took the ball and fed Johnson on his left.
Despite a heavy first touch, Johnson managed to slip the ball to an open Dunfield, who easily tapped into the empty net after goalkeeper Manuel Gonzalez came off his line to challenge Johnson.
It was the Toronto FC captain's second Champions League goal.
Toronto, which has scored two or more goals in six of its last seven CONCACAF Champions League road matches, threatened to add a third in the 75th minute. But Johnson hammered a first-time shot off the crossbar from eight meters following a cross from an open Reggie Lambe.
Four minutes later, Amarikwa dispossessed Deris Umanzor and raced in on goal, but his acute-angled shot slid across the face of goal and wide.
Off another turnover, Andrew Wiedeman's first touch on the ball since coming on for Lambe was high and wide of the far post in the 81st minute.
Two minutes later, Wiederman turned provider, setting up Johnson, whose first-time shot was saved by a diving Gonzalez.
Dunfield put the finishing touches on a quality road win with his second of the game, sliding in to push Ashtone Morgan's low cross into the net with four minutes remaining.
Aguila, which lost all four of its group stage matches and were outscored 17-1, were without four influential players: Benji Villalobos, Osael Romero, Isidro Gutierrez and Mardoqueo Henriquez - all of whom have joined the Salvadoran national team for training in preparation for its next World Cup qualifiers.