Jamiro Monteiro tallied a goal and an assist, Mark McKenzie scored a goal and Kacper Przybylko and Kai Wagner added two assists each for Philadelphia, who stretched their unbeaten streak to five straight and are 7-0 at home on the season.
The Union and Toronto each have 41 points, but the Union are in first thanks to a better goal differential. Philadelphia are now 12-3-5 on the season.
Toronto FC had their nine-game unbeaten streak snapped and dropped to 12-3-5.
Philadelphia dominated play in the first half as Przybylko had a great scoring chance in the sixth minute but his header went just wide.
Santos made it 1-0 in the 27th minute on a header from inside the box and Przybylko set up McKenzie for a goal seven minutes later.
The Union kept pressing in the second half as Monteiro made it 3-0 by blasting a shot from the top of the box just under the crossbar.
Santos scored in the 63rd minute and completed his hat trick in the 68th by tapping in a pass from teammate Brenden Aaronson.
