The goal was his fifth in the Premier League after the summer transfer from Sporting Lisbon and the first since November 1.
Gyökeres was injured in the same match, against Burnley, and missed four games. Once fit again, he went scoreless in five games – mostly as a substitute – for the league leaders.
Arsenal were penalised for a clear handball on an Everton player in the 27th minute, but only after a VAR check. Team captain Martin Ødegaard first handled the ball and then passed it to Gyökeres.
England national team goalkeeper Jordan Pickford went in the right direction, but was nowhere near stopping the hard-hit penalty.
Leandro Trossard hit the post just before Gyökeres came off after 65 minutes and was replaced by Gabriel Jesus.
Arsenal remain top of the Premier League, two points ahead of Manchester City.
In the evening's second match, bottom team Leeds, with international defender Gabriel Gudmundsson in the starting eleven, took an important victory – a clear 4–1 at home against Crystal Palace. Leeds now have a margin of six points below the relegation zone.
