If it was a bleak day for Manchester United in the English title showdown, it was an afternoon to remember for Bayern Munich, who won at Schalke in Germany's battle of the top two, displacing the leaders and building their confidence for Wednesday's game at Old Trafford.

Bayern won 2-1 despite having Hamit Altintop sent off for a second bookable offence in the first half. Their manager, Louis van Gaal, said: "It was an outstanding performance. We didn't concede many chances and scored two beautiful goals. I'm very satisfied.

"Naturally it's very positive that we have won here. United have lost at home, we won away from home. But we need to have a rest, have a bit of treatment, and then see who will be available for Wednesday."

The French winger Franck Ribéry gave Bayern the lead, Thomas Müller took advantage of Rafinha's defensive lapse 70 seconds later and, although Kevin Kuranyi pulled a goal back for Schalke after 31 minutes, Bayern held on to go top. There was even more good news for Van Gaal's team: Arjen Robben, their outstanding performer over the season, was not in the squad but the Dutch winger is expected to recover in time for the second leg.

So Bayern will arrive in Manchester not just with a deserved lead, but with a stronger team than they had for last week's 2-1 win. It looks tough for United, but Sir Alex Ferguson was still in a relaxed mood as he looked ahead to the match – admittedly before the Chelsea defeat. When informed of a rumour that some bookmakers were willing to offer 66-1 against a Rooney-less England winning the World Cup, Ferguson bit like a perch. "You means the odds were originally less than that?" he asked. "I find that hard to believe. 66-1 sounds like a fair price to me."

This is the sharp end of Manchester United's season, and despite losing his star player against Chelsea and Bayern, Ferguson was still able to joke about it. Partly because he is such an experienced campaigner, but mostly because the news on Rooney could have been much worse. Ferguson has already pencilled him in for a return against Manchester City on 17 April and expects to have him available for the Champions League semi-finals at the end of the month should United qualify.

"I think Wayne will be back in three weeks at the most," Ferguson said. "City away seems the most likely game. He's already been on the bike and the water-treadmill. He'll be working every day until we get to a point where we can get him on the training field. He's an enthusiastic lad but he's sensible about these things. He'll not be getting carried away or rushing himself back, he'll listen to the medical people because he knows it's important to get back without doing any further damage. There's no reason why he shouldn't play in the semi-finals in Europe, as long as we get that far."

Keenly aware that United have never beaten Bayern outside of a European Cup final, Ferguson respects the German team's ability to impose themselves on a game without necessarily overrunning their opponents.

"The first leg wasn't one of our better performances, because we didn't pass the ball well," he said. "Bayern didn't cause us too many problems in terms of penetration, they never really opened us up, but what they did was keep us on the edge of our box for long periods, so we never got up the pitch."

Ferguson is likely to recall Antonio Valencia for the second leg, after admitting that his decision to play Park Ji-sung had not come off in Munich.

"I'm sure we can score in the home leg. We've been in this situation before, we have the experience, and that away goal does mean something. Our performance level at home has been good, especially when the chips are down. There are areas we can try to exploit. I don't think Bayern are the quickest at the back, even their midfield isn't that quick. They deserved to win the first leg, they were highly motivated and well-prepared, and you have to congratulate their coach for that. Wednesday will be different. We'll be the ones motivated."