Union goalkeeper Andre Blake made three saves and earned his seventh shutout of the season.
The Union (9-3-4, 31 points) won their fifth straight home game.
FC Cincinnati, which fell to 3-9-4 (13 points), failed to score one goal in two meetings against the Union this season.
FC Cincinnati had the first strong scoring chance when designated player Yuya Kubo found himself wide open at the top of the box. But Kubo shot the ball over the goal in the ninth minute.
In the 25th minute, Philadelphia created a solid opportunity as Anthony Fontana fired a right-footed shot from just inside the box. FC Cincinnati goalkeeper Przemyslaw Tyton made a diving save to keep the game scoreless.
FC Cincinnati was able to generate very little offensively and still has scored only one goal in the first half all season. They nearly took the lead, however, as Joe-Claude Gyau had a point-blank shot saved by Blake in the fourth of five minutes of stoppage time.
The Union received an early second-half corner kick in the 51st minute yet couldn't come up with a shot after the ball bounced around the box.
The Union stayed aggressive and finally went ahead 1-0 in the 59th minute when Ilsinho hit a shot off FC Cincinnati's Maikel van der Werff and into the goal.
Philadelphia took a 2-0 lead in the 73rd minute when Aaronson left a crisp pass for Bedoya in front and he scored his third goal of the season.
Elliott headed home a cross in the 79th minute for his first goal of the season and the three-goal Philadelphia lead.