The English champions needed to overturn a 3-2 deficit following the first leg of their last-16 tie at Old Trafford last week – but Fernando Llorente’s 23rd-minute volley handed the La Liga outfit an early lead and made United’s task much more difficult.
Bilbao then sealed their progression into the quarter-finals courtesy of Oscar de Marcos’s deflected goal after 65 minutes, with Wayne Rooney’s stunning strike merely a consolation.
“There are always lessons to learn from every football match, whether you win or lose,” said Ferguson.
“It’s disappointing more than anything. We haven’t progressed in the Champions League and now we’re out of the Europa League. I think the best team went through. I don’t think we can complain.”
With the Premier League title now United’s only chance of silverware this term, the 70-year-old added: “It’s not a sense of relief going out of Europe because we still have 10 games to play in the league and that’s a long way to go until you can win a title.
“Obviously we now have to make sure we win on Sunday against Wolverhampton Wanderers.
“We decided to take off Rio Ferdinand, Michael Carrick and, eventually, Ryan Giggs because we have to think about Sunday.”
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