Toronto FC (9-2-4, 31 points) is unbeaten over its last five games, going 4-0-1 during the span.
Sergio Santos scored the lone goal for the Union (8-3-4, 28 points). Philadelphia had been unbeaten in five straight (4-0-1) heading into the match.
Toronto had to rally from an early 1-0 deficit.
The win for the Reds came at a cost as Jozy Altidored appeared to injure his left hamstring in the 51st minute and he was quickly sent off for the remainder of the game. Nick DeLeon came in as a substitute for Altidore.
"It looks like a minor hamstring issue," Toronto manager Greg Vanney said. "He says that soreness is there. We'll have to see. We won't know what the time frame looks like until we get a scan and a sense of what it is."
A couple of minutes after Philadelphia's Matt Real misfired on a solid scoring chance in the box, Toronto FC capitalized with the equalizer in the 58th minute as Akinola scored his seventh goal of the season.
Toronto FC continued with their stellar offensive pressure and took a 2-1 lead in the 76th minute as a wide open Pozuelo headed a shot past Union goalkeeper Andre Blake. Pozuelo scored a goal for the sixth time in the last eight games and has seven overall.
The Union struggled to create scoring opportunities in the final five minutes. In the first of four minutes of stoppage time, Alejandro Bedoya made a long run and headed a cross on goal but Toronto goalkeeper Quentin Westberg was in position to make the save.
The Union struck quickly for a 1-0 lead in the fifth minute when Santos dribbled through three Toronto FC defenders and chipped a left-footed shot past Westberg. It was Santos' third goal of the season.
In the seventh minute, Toronto FC nearly tied the game as Chris Mavinga received a pass directly in front but had his point blank shot saved by Blake.
Philadelphia's Jamiro Monteiro ripped a shot from about 30 yards out in the 30th minute and a leaping Westberg tipped the ball off the crossbar.
Toronto FC had a huge edge in possession in the first half with the ball 65 percent of the time. But they trailed 1-0 heading into the locker room.