The Brazilian substitute leapt high to head home at the back post in the 85th minute from Olivier Mbaizo's cross.
Despite being reduced to 10 men after goalkeeper Matthew Freese's inexplicable red card, Philadelphia were good value for a draw, edging possession 54-46 per cent and having more shots on target (7-3).
The Red Bulls had been hoping to move up as high as third spot in the Eastern Conference and looked on track when Patryk Klimala put them ahead from the spot.
New York won the penalty when Freese made a comical error, trying to dribble past Wikelman Carmona from a backpass.
Freese's touch was poor, opening the door for Carmona to tap in, with the keeper resorting to tackling the Red Bulls midfielder for a clear-cut penalty and red card.
Polish midfielder Klimala sent substitute keeper Joe Bendik the wrong way from the spot, but New York would be denied late by Santos' pinpoint header.
Philadelphia, remains winless from its past three games, but are third, four points behind Eastern Conference leader New England. The Red Bulls stay seventh.
Nashville moved up to fifth with a 2-2 home draw against 10-man Atlanta United.
United had opened the scoring after captain Anton Walkes' fifth-minute header but Nashville replied with Hany Mukhtar setting up Jalil Anibaba to equalize before netting a 48th-minute penalty following Erick Torres' handball.
Atlanta's teenage substitute Jackson Conway equalized shortly prior to the hour mark but United were forced to hang on with Irish defender Jake Mulraney sent off late.