The visitors looked likely to stretch their lead at the top of the MLS Eastern Conference to seven points, despite being second best for much of the game.
However, Robbie Keane dispatched both spot kicks to see Bruce Arena's men jump above Houston Dynamo to the top of the Western Conference.
It was the hosts who had the run of the play throughout the game, but they struggled to find a way past Andy Gruenebaum, as well as suffering from wasteful finishing.
That looked like it might settle matters, but the hosts were handed a lifeline when Gruenbaum brought down Jose Villarreal inside the area.
Keane stepped up and made no mistake. It was the Irish striker who was felled by Anor to win the second penalty two minutes into injury time.
After dusting himself off, he once again found the net to seal all three points.