Sunday's match was the first of four consecutive home games for the Union. On Wednesday, they will host Sporting Kansas City in the Open Cup semifinals.
The Union (5-9-2) have won three league games under interim head coach John Hackworth, taking four of their last six overall - including Wednesday's 2-1 victory over the Los Angeles Galaxy. The back-to-back MLS wins were the team's first since April.
"I think everybody is just comfortable," defender Sheanon Williams said of the feeling in the locker room under Hackworth. "I think everyone is playing freely, and that's been good for us. That's what we've been needing."
Toronto, the last-place team in the Eastern Conference with a 2-11-4 record, had beaten the Union, 1-0, in their previous meeting, on May 26.
"I just think it is a confidence factor," forward Freddy Adu said. "We're not a very big team. We have to do what works for us. And today everybody brought it."
McInerney had a chance in the second minute, but his cross from 10 yards out went into Toronto goalkeeper Milos Kocic's hands.
In the 13th minute, back-to-back shots by Adu were blocked by defenders at close range after he beat a couple of Toronto defensemen one-on-one. McInerney had a chance to break the game open in the 15th, but Kocic made a diving save. Together, McInerney and Adu combined for several offensive chances.
The chances kept coming in the first half for the Union. A free kick from Adu found Lionard Pajoy's head but went wide of the net. In the first 45 minutes of play, the Union had 11 shots, three on goal, to Toronto FC's four. They also dominated possession, controlling the ball for 70 percent of the half.
It wasn't until the 34th minute that McInerney's cross found midfielder Gabriel Gomez just outside the 6-yard line. Two minutes later, a streaking Adu was on the receiving end of a pass from Gabriel Farfan, who had received the ball from McInerney. Adu put the ball just under the hands of Kocic, giving the Union a 2-0 lead with less than 10 minutes to play in the half.
"Today was just one of those days where my teammates did a great job of finding me in dangerous spots, and when I did get the ball, I was aggressive," Adu said. "That's what I felt like I haven't been the past few games - aggressive."
In the second half, Hoppenot, who went in for McInerney in the 65th minute, chased down a through ball from Michael Farfan and scored. The goal, in the 78th minute, came on Farfan's second assist of the game and boosted the Union's lead to 3-0.
Williams had a header on the goal line with less than 10 to play to preserve Zac McMath's shutout.