While dominant Bayern wrapped up the Bundesliga title in record quick time, United are seventh in the Premier League having endured their worst season for 24 years following David Moyes' appointment to replace the retired Alex Ferguson.
"Manchester United are one of the world's best teams. It doesn't matter what situation they're in right now," Guardiola, also in his first season at the club, told a news conference in Manchester on Monday.
"United have good players. These two games could be the best two performances of their season. They can beat us."
Guardiola, who joined Bayern having taken a year off after leaving Barcelona following a host of trophies, was coy over whether he had ever been approached over replacing the hugely successful Ferguson.
"Maybe I didn't understand if I received an offer," he said, apparently joking over Ferguson's thick Scottish accent and speed of talking.
He did though have sympathy for former Everton boss Moyes, who has been the subject of protests from some fans aghast at United's decline a season after winning the Premier League.
"I could also be in his situation one day. Football is a fast-moving business these days," Guardiola added.
Holders Bayern easily dispatched Arsenal in the last 16, winning 2-0 in England, but Guardiola is expecting a tough encounter at Old Trafford and is keeping his cards close to his chest over his lineup.
Thiago Alcantara is out injured but fellow midfieder Toni Kroos, who media reports say is a transfer target for United amid a Bayern contract wrangle, is not guaranteed a start despite impressing against the Gunners.
"Tony Kroos played very well against Arsenal but this is another game and anything can happen," Guardiola added.
Bayern goalkeeper Manuel Neuer, courted by Ferguson after a stunning display for Schalke 04 against United in 2011 before joining the German giants, cited their display in the last round as proof the English champions were still a big threat.
United lost 2-0 at Olympiakos but stormed back at home to win 3-2 on aggregate, although hat-trick hero Robin van Persie misses both legs against Bayern with a knee injury.
"The name Manchester United deserves a lot of respect alone. They fought back well against Olympiakos," the Germany number one said.
"We know just how well United can maintain their focus."
- Sports & Recreation
- Manchester United
- Premier League
- Alex Ferguson
- David Moyes