Tensions flared after Declan Rice scored West Ham’s first goal, when visiting fans, who had been goading the Hammers support since before kick-off, tried to climb over hoardings to get across to the home section.
Police and stewards managed to keep them at bay, but there were further skirmishes at the final whistle with plastic bottles thrown between rival fans.
The Metropolitan Police said: “There were three arrests; two for assault of an emergency services worker and one for possession of an offensive weapon.”
There was also an angry post-match altercation between supporter liaison staff from both clubs in the bowels of the stadium, with Rapid’s eventually being marched off the premises.
Uefa has said it will be studying the incidents from during and after the match, as will the police in conjunction with West Ham.
Said Benrahma’s late goal wrapped up the 2-0 win for West Ham to leave them top of Group H after two matches.