Le Toux scored his team-leading eighth goal of the year.
"I just want us to win games, and if I score, that is a good thing," he said.
It looked like a shutout for the Union after Chicago midfielder Jeff Larentowicz, a former Chestnut Hill Academy star, managed to get free deep in the penalty box and headed in a corner kick from Harry Shipp in the 60th minute. He sandwiched the ball between Le Toux and goalie Zac MacMath.
"The guys have to fight through and communicate and sort it out quicker," interim coach Jim Curtin said. "Jeff got a lot on it, but you would like to see someone jump with him."
The tone for the Union's night was set in the 12th and 13th minutes, when Le Toux had three straight corner kicks but the Union could not convert. On the second chance, forward Conor Casey barely missed on a header. Moments later, defender Sheanon Williams was open near the edge of the penalty box, but he couldn't handle the ball.
This was the second consecutive dramatic finish in a road match against Chicago. In April, MacMath saved a penalty - and the rebound - in the waning moments to preserve a 2-2 draw.
Union midfielder Cristian Maidana missed the match with a left-hamstring injury suffered during Wednesday's victory over New York.