A brace from Amad Diallo gave United their first success in this season's competition, coming under interim manager Ruud van Nistelrooy after they had drawn the previous three games with Erik ten Hag was in charge.
Tottenham Hotspur made it three wins from three in the Europa League with a 1-0 win at home to AZ on Thursday but Manchester United remain winless after being held to a 1-1 draw at red-carded Jose Mourinho's Fenerbahce.
Manchester United manager Erik ten Hag has highlighted a lack of goals as the major factor behind the English giants' faltering start to the season.
Manchester United manager Erik ten Hag said his side had failed to maintain their intensity in Wednesday's 1-1 Europa League draw with FC Twente and should have pushed to kill the visitors off before they had the chance to equalise.
Erik ten Hag made a convincing case to be spared the sack as Manchester United upset Manchester City to take the FA Cup with a shock 2-1 victory in Saturday's final.
Leverkusen - or 'Neverlusen' as they had been dubbed after obliterating Bayern Munich's 11-year Bundesliga title monopoly in Germany - can still win a domestic double with victory against second-tier Kaiserslautern in Saturday's German Cup final.
Gian Piero Gasperini lavished praise on his "incredible" Atalanta players after they stunned Bayer Leverkusen to win the Europa League and claim their first ever continental honour.
Ademola Lookman scored a stunning hattrick as Atalanta ended Bayer Leverkusen's 51-match unbeaten run to win the Europa League final 3-0 on Wednesday and claim their first trophy for 61 years.
Bayer Leverkusen had won only two major trophies in their 119-year history before this season but on Wednesday the newly-crowned Bundesliga champions have the chance to claim a double when they face Atalanta in the Europa League final in Dublin.
Leverkusen, the Bundesliga champions who have also reached the May 25 German Cup final, played their 49th match without defeat in all competitions, surpassing Benfica's long-standing European record set from 1963 to 1965.
Atalanta's passage to the Dublin final, where they will face Bayer Leverkusen, later this month was fully deserved after a dominant performance in which Marseille barely had a kick in yet another poor away display from the Ligue 1 outfit.
Xabi Alonso's Leverkusen, who have 40 wins in their unbeaten run, face Atalanta in the May 22 final in Dublin after the Italians comfortably got past Olympique Marseille.
Xabi Alonso's rampaging Bayer Leverkusen will have an additional incentive in Thursday's home second-leg Europa League semifinal against Roma: breaking a 59-year-old European football record.
Erik ten Hag insists he is the man to revive embattled Manchester United after they hit a new low against Crystal Palace. But will he even be there for the FA Cup final?
Leverkusen's superiority was fully on display.
"Disappointed that we did not go through but not frustrated or angry. Now we can focus on the league and that's what we will do," Klopp told reporters.
Last season's runners-up Roma advanced to their fourth European semi-final in a row.
Atalanta have a chance to make history on Thursday as they welcome Liverpool to Bergamo with one foot in the Europa League semi-finals thanks to a stunning first-leg win at Anfield.
Jurgen Klopp was headed for a glorious send-off in his final season at Liverpool just a few weeks ago, but talk of a potential quadruple is now long forgotten as the Reds have come off the rails.