The victory kept Toronto FC in second place in Group 1 with six points, three back of their next opponent — first-place Santos Laguna.
Aguila finished last in the three-team group with zero points from four games. Only the top team from each group advances to the next round.
Forward Quincy Amarikwa had the other goal for Toronto, opening the scoring in 16th minute by heading in a cross from Ryan Johnson.
Johnson also assisted on Dunfield's first of the night with TFC converting on a 3-on-1 off a turnover. The Jamaican international charged in on goalie Jose Gonzalez on the left side before crossing it to Dunfield for an easy goal in the 40th.
Johnson also belted a shot off the crossbar from in close in the 74th minute at Estadio Cuscatlan.
Dunfield put the game out of reach in 86th with his second of the night.
It was TFC's first victory in all competitions since routing Aguila 5-1 in the first meeting between the clubs on Aug. 1 at BMO Field.
Having lost 3-1 at home to Santos, Toronto needs to win in Torreon, Mexico, by more than two goals to reach the quarter-finals for a second straight year when the teams meet Oct. 24.
Toronto FC were missing defender Richard Eckersley after he collided with an L.A. Galaxy player on Saturday in an MLS game at the Home Depot Center.