The Red Bulls (8-11-7, 31 points) pushed their unbeaten streak to four games (2-0-2) to match a season high thanks to Fernandez's third goal in four games.
After scoring a big goal in the 43rd minute in Saturday's 1-0 win at Yankee Stadium against host New York City FC, Fernandez came through again in impressive fashion on a physical night when the teams combined for 27 fouls and six yellow cards.
Fernandez leveled the game with an impressive sequence late in the first half. Under pressure by two defenders in the center of the box after getting a pass from Cristian Casseres Jr., he had his back to the net but was able to quickly turn around and fire a right-footed shot into the bottom right corner.
Fernandez's tying goal occurred after Sergio Santos scored in the 16th minute for Philadelphia (10-7-9, 39 points).
Santos got his second goal against the Red Bulls this season when he got the ball off a scramble following a corner kick. He finished off the play by tapping the ball into the center of the net with a right-footed shot.
Santos nearly scored his second goal of the match in the 72nd minute when he converted a feed from Leon Flach. The goal was quickly waved off due to an offsides call and was upheld following a quick video review.
Red Bulls goalkeeper Carlos Coronel made one save and also had the long ball that ultimately resulted in Fernandez's tying tally.
Philadelphia goalkeeper Andre Blake stopped three shots.