However, at 2-0 and with 13 minutes remaining, Higuain had the chance to set up a tense finale when Inter Miami were awarded a penalty, but the Argentina forward blazed his kick over the bar before he clashed with Union defenders, who appeared to celebrate his miss.
The Union (8-2-4, 28 points) picked up three points in heavy rain without captain and midfielder Alejandro Bedoya (suspension for yellow-card accumulation) and right-back Ray Gaddis (hamstring). Union goalkeeper Andre Blake made three saves for shutout, his sixth of the season.
Inter Miami (3-9-2, 11 points) maintained ball possession for 59.4 percent of the game but couldn't beat Blake.
In the 20th minute, Higuain received a cross in the box and sent a bicycle kick off the post.
The Union took a 1-0 lead in the 25th minute when Fontana ripped a shot into the upper corner of the goal for his fourth of the season.
Higuain had another strong scoring chance in the 36th minute, but Blake was able to clear the ball after a shot from the corner of the goal.
Inter Miami nearly scored in the 62nd minute when Ben Sweat sent a bending shot toward the upper corner of the net. Blake was able to tip the ball just wide.
The Union extended their lead to 2-0 in the 69th minute when second-half substitute Ilsinho tapped a shot past Robles directly in front.
After a video review, Inter Miami were awarded a penalty kick for a handball on Przybylko in the box. In the 77th minute, Higuain shot the penalty kick over the goal and appeared visibly frustrated.
Nine minutes of stoppage time was added on at the end, and Aaronson capitalized to score the Union's third goal in the 97th minute. Aaronson, 19, reportedly reached a deal this week to join RB Salzburg in Austria following the current MLS season.