Police had to intervene to separate the two sets of supporters and the Belgian side said their fans' behaviour was unacceptable. One Anderlecht fan was apprehended by security after running onto the pitch.
"The club will take this onwards with supporters because we don't tolerate this kind of behaviour, not in our home stadium and not away," a spokesperson for Anderlecht said.
"We will take it up with the fans and definitely UEFA and we strongly condemn this. We want to apologise to West Ham for this behaviour."
West Ham manager David Moyes praised Anderlecht's response.
"It's very good of the club to come out and say it. Big credit to them," Moyes told reporters.
"I think everybody's focus gets taken away when there's crowd trouble in some way. The players' job is to get on with it and I thought they did.
"We are in a different society, a different world now and it's not what any football club wants to have connected to them ..."
