After a dismal domestic campaign by their lofty standards - United sit seventh in the Premier League, seven points behind fourth-placed Arsenal - their last realistic chance of qualifying for next season's Champions League rested on winning the competition.
Should they fail to qualify, it will be the first time in 18 seasons in which they have not had a place in Europe's premier competition and Moyes hopes their hiatus can be limited to one season.
"We've got to get Champions League football," Moyes told Sky Sports after a 3-1 second leg defeat knocked United out 4-2 on aggregate. "That's the way it looks but I believe it's not far away.
"It'll hopefully only be one year the way we hope to rebuild. The focus now is on getting a team that can get us back in this competition because we've really enjoyed it."
United briefly looked like they were going to cause an upset after Patrice Evra blasted them in front in the 57th minute.
That lead lasted for just one minute as holders Bayern equalised through Mario Mandzukic before Thomas Mueller and Arjen Robben sealed the win.
Moyes praised his team's efforts but was quick to shift the focus back to the job at hand.
"We'll regroup and we'll start building towards being in this competition again," the Scot added. "My job is just to get on and do the job. My focus is on getting a side that gets us back in the Champions league and that's going to be our objective now."
Alex Ferguson's successor took over an ageing squad at the start of the campaign and a major overhaul appears his priority.
United failed to sign a number of transfer targets last summer, including Barcelona midfielder Cesc Fabregas, and the lack of European football and a perception that the club is heading in the wrong direction could make it difficult for Moyes to attract the calibre of players required.
However, the 50-year-old was adamant luring players to Old Trafford would not be an issue.
"That's never been a question, we're looking to spend the right money on the right players if they're available.
"Any players that I've quietly discussed with would be happy to join Manchester United.
"There's who quietly want to come because they know its a short thing, not a long thing. They're all very keen to join such a great club."
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