Arsenal were 2-0 up at home to Palace inside nine minutes with goals from Sokratis Papastathopoulos and David Luiz.
Palace halved the deficit when Luka Milivojevic scored from the spot following a VAR intervention after referee Martin Atkinson had initially booked Wilfried Zaha for diving.
Jordan Ayew headed Palace level in the 52nd minute but VAR was again in action when Sokratis thought he had won it for the hosts in the dying minutes but his effort was ruled out for a foul by Callum Chambers on Gary Cahill.
Listen to Unai Enery talking after yesterday’s game
It left Arsenal four points behind fourth-placed Chelsea who won at Burnley on Saturday. Palace are sixth.
“For me there is no confusion — it is not a good decision,” Arsenal manager Unai Emery said.
“We deserved to win, we had a good reaction after they equalised, we scored but then they didn’t count it.”