But the Orlando advantage was wiped out with only seconds remaining, after referee Baldomero Toledo called a handball on Orlando midfielder Servando Carrasco, an equally debateable decision considering the ball his hit shoulder.
The referee originally awarded a free kick just outside the box, but changed his call after consulting an official and awarded a penalty.
The decision allowed Lee Nguyen to convert a spot kick for New England and tie it up for the visitors.
The raucous crowd then rained debris onto the field and there was a fiery exchange between coaches Jay Heaps and Adrian Heath and officials as teams left the arena.
"There was a lot of emotion at the end but I thought it was a really good battle between two good teams," Revolution coach Heaps told reporters. "I was trying to tell the referee there was stuff being thrown on the field and I was worried for my players' safety. It felt like things had spiralled out of control.
"Adrian (Heath) was upset with me and I was upset with him for not letting me protect my players.
"But we also felt there was a clear handball on their second goal, and then the handball at the other end clearly happened in the box, so it had to be a penalty-kick call. From my vantage point, I saw two clear handballs.”
For Heath, it was a rollercoaster, but he remained positive as the Lions sit just three points off top spot in the Eastern Conference.
"You think you’ve won the game in the end when you score that late, and the players probably thought that would’ve been it too," he said.
"But I can’t fault them for their efforts in the second half. I thought we played with a lot of passion, if not with a lot of quality at times, especially the first half.”
Earlier, Orlando captain Kaka was awarded a contentious penalty after only 11 seconds that led to the opening goal.
Elsewhere, FC Dallas came back from a goal down to beat Kansas City 2-1 and push to a three-point advantage on top of the Western Conference.
(Reporting by Ben Everill in Los Angeles; Editing by Andrew Both)
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