The Three Lions were 1-0 down before Bellingham equalized in the 95th minute, with Harry Kane going on to score the winner.
A UEFA spokesperson said: “Ethics and Disciplinary Inspector will conduct a disciplinary investigation regarding a potential violation of the basic rules of decent conduct by the English FA player, Jude Bellingham, having allegedly occurred in the scope of this match.”
Bellingham appeared to gesture in the direction of the crowd, before mouthing “who else” in reference to himself.
The Real Madrid star may be banned if found guilty, as FIFA rules state: "Anyone who insults someone in any way, especially by using offensive gestures or language, or who violates the principles of fair pay or whose behavior is unsporting in any other way may be subject to sanctions in accordance with art. 10 ff."
Bellingham wrote on social media post-game: "An inside joke gesture towards some close friends who were at the game. Nothing but respect for how that Slovakia team played tonight."