The visitors took the lead in the second minute of the game as Matias Laba won the ball in midfield and drove the length of the field, beating the challenge of Stephen McCarthy before slotting his effort past Bobby Shuttleworth.
New England almost found an equaliser in the 13th minute when Joe Bendik pushed Dimitry Imbongo's effort into the path of Diego Fagundez, who hit a first-time volley, but Ashtone Morgan was on hand on the line to clear.
Fagundez saw another shot cleared off the line as he tried to bundle the ball home; this time Richard Eckersley managed to get his boot to his trickling shot to maintain Toronto's lead.
After the break, the midfielder was denied yet again as he raided into the penalty area, but this time Bendik got a big hand to his shot to keep it out of the net.
With time running out, New England won a free kick on the right, which was whipped in dangerously by Lee Nguyen and Fagundez met it first time on the volley, but his effort crashed off the bar and went over as his side fell to defeat.