The decision came following a challenge by Nick Pope on Viktor Gyokeres. Referee Jarred Gillett initially awarded the penalty but, after consulting the VAR review screen, reversed his call.
Despite the controversy, the Gunners secured a 2-1 victory thanks to a last-minute header from Gabriel. The England international, however, remained disappointed with the decision to cancel the early penalty.
"There are a few things we can speak about, for example the penalty,” said Saka.
"For me if we have VAR, it is for a clear and obvious error and the fact that it took the ref that long to decide shows it is not a clear and obvious error.
"It is things like this that always go against us, but today we got what we deserved and that's why we are all so happy. It doesn't matter now, does it?"