Bellingham scored an astonishing 95th-minute equaliser to push the game into extra time, gesturing after his goal at England fans who had been critical, then making the crotch gesture following the final whistle with the game won 2-1.
"A UEFA Ethics and Disciplinary Inspector will conduct a disciplinary investigation regarding a potential violation of the basic rules of decent conduct by the English Football Association player, Jude Bellingham, having allegedly occurred in the scope of this match," UEFA said in a statement on Monday.
While Bellingham's aggressive goal celebration was clearly an angry message to England fans, the crotch gesture was viewed by some spectators as an insult to Slovakia.
Bellingham, however, said on social media that he was having a laugh with friends.
"An inside joke gesture towards some close friends who were at the game. Nothing but respect for how that Slovakia team played tonight," he said.
There was no immediate reaction from Bellingham or the English Football Association to UEFA's statement.
The Real Madrid player has been showered with praise in the past for his maturity, but acknowledged after the Slovakia game that he felt an explosion of emotion after his bicycle-kick goal, given days of heavy criticism of England on social media.
"People talk a lot of rubbish and it's nice that, when you deliver, you can give them a little bit back," he told reporters shortly after the game in Gelsenkirchen on Sunday.
He was walking alongside captain and fellow goalscorer Harry Kane when he kissed his hand and lowered it to his groin, according to footage of the players at the end of the game.
UEFA also said it was charging England's FA for their fans' lighting of fireworks and other disorder.
European football's body has an array of possible sanctions at its disposal from fines to suspensions. Albania's Mirlind Daku was banned for two games after leading fans in offensive chants.
England, who have put in strangely tepid and disjointed displays despite being among the pre-tournament favourite, face Switzerland in the quarter-finals on Saturday.