Goals to Daniel Gazdag and Cory Burke handed Union the three points to put it on 36 for the season, leading the Eastern Conference by a solitary point.
Gazdag's penalty in the 26th minute was critical, because from there Union could absorb pressure, and the best defence in the MLS was able to grind out another win.
With only 35.7 per cent possession in the second half, Union's job was simpler after Burke doubled the margin in the 66th minute, heading in Kai Wagner's dead ball at the back post.
In only his second start since Inter's 3-1 loss to Houston Dynamo in April, Gonzalo Higuain bagged his third goal of the season – smashing the ball into the top corner from distance on the run, and on his opposite left foot – but it was mere consolation in the 82nd minute.
New York City remains hot on Union's heels, however, maintaining the one-point gap in the Eastern Conference after claiming a tough 1-0 win away to FC Dallas.
Heber was left with a simple tap-in in the 29th minute after Santiago Rodriguez was able to drive into space from the second ball, and he coolly finished for the eventual three points.
Elsewhere in the East, a Jhon Duran brace handed Chicago Fire a 2-0 victory over Toronto FC.
While D.C. United twice equalised in the final 10 minutes to snatch a 2-2 draw at home to Columbus Crew.
Cincinnati and Orlando City dropped critical points in the playoff race with respective draws to the Vancouver Whitecaps and Colorado Rapids, while a Ronaldo Cisneros brace gave Atlanta United a big 2-1 win over Real Salt Lake, putting it three points behind seventh-placed Charlotte.
Most of the chasing pack in the Western Conference were not able to capitalise on Dallas and RSL's slip-ups, with Minnesota United playing out a 1-1 draw with Sporting KC, while San Jose Earthquakes scored a 3-2 win away to Los Angeles Galaxy.
Nashville SC did capitalise and moved to third in the West though, claiming a 1-0 win at home to the in-form Seattle Sounders.
Hany Mukhtar scored the eventual winner in the 44th minute with the interval beckoning, scoring in transition after Randall Leal snatched the ball and released CJ Sapong.