A positive night for Villa - which gave them a seventh straight home win - was marred by trouble from travelling fans, who have a history of causing problems.
Malen took his tally for the season to six to give Villa a deserved two-goal lead at the break, but that resulted in the home players - including the scorer - being pelted by objects thrown by visiting supporters.
Orchestrated clapping and singing turned ugly when Young Boys fell behind and the game was stopped for five minutes as fans clashed with police in the Doug Ellis Stand and even needed captain Loris Benito to calm them down.
Dozens of police officers were deployed in riot gear in front of the away end and no further trouble occurred after the interval.
Young Boys supporters were fined E28,250 ($A50,000) for similar issues at Manchester City a couple of years ago and around E18,000 ($A32,000) for the use of pyrotechnics at Celtic in February.
The action on the pitch played second fiddle for a while and Joel Monteiro's late consolation did not stop Villa from earning a fourth win from five in the competition as their superb form continued.
Manager Unai Emery said Malen was improving rapidly.
"He's progressively getting better. He is doing his tasks over his goals and for me the most important thing is how he is working, how he is getting fit and better.
"He's helping us and really performing very good and keeps going."
In England, hosts Nottingham Forest paid tribute to their 1979 European Cup-winning heroes in style with a 3-0 win over Malmo.
Brian Clough's Forest conquered Europe 46 years ago when Trevor Francis's goal against the Swedish side gave them a 1-0 success in Munich.
Nostalgia was in full supply ahead of kick-off, with most of the living players from that famous night paraded on the City Ground pitch as well as a two-minute film projected onto the Brian Clough Stand.
And although the stakes were much lower this time in a league phase match, Forest were again victorious thanks to goals from Ryan Yates, Arnaud Kalimuendo and Nikola Milenkovic.
In some of the other Europa action, Porto beat Nice 3-0, Feyenoord went down 3-1 at home to Celtic, Roma defeated Midtjylland 2-1, Lyon thrashed Maccabi Tel Aviv 6-0 and Rangers drew 1-1 with Braga.
In the Conference League, Crystal Palace came unstuck in Strasbourg as they slipped to a 2-1 defeat.
Tyrick Mitchell's first-half goal had put the Eagles on course for a third win from four European matches.
But they were pegged back by Chelsea-bound striker Emanuel Emegha and then sent packing by a first senior goal from teenager Samir El Mourabet.
Fiorentina also lost, going down 1-0 to AEK Athens with Mijat Gacinovic scoring.
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