Zinedine Zidane's side started complacently at the Santiago Bernabeu and ended frantically, with Cristiano Ronaldo's 87th-minute equaliser cancelling out a delightful early chip from Athletic's Inaki Williams in between.
Barcelona's commanding lead at the top of La Liga, which now stands at 12 points over Atletico Madrid and 15 on Real, means these matches carry reduced significance and inevitably lack a certain edge.
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But Zidane may at least be concerned by a loss of momentum, particularly given this side is likely to be very close to the one that starts the semi-final first leg at the Allianz Arena in a week's time.
Real have managed to hit a different gear in the Champions League knock-out stages but this draw means they have now won only once in their last four matches, having strung together 11 victories from their previous 12.
Ronaldo's late flick was his 22nd goal in 12 games and with the Portuguese in this sort of form, almost any performance can be salvaged.
But Real's night was better summed up by one moment in the second half when Sergio Ramos repeatedly failed to clear and then turned to face the crowd's jeers with his arms outstretched. The jeers grew louder.
If the Real team that faced Malaga on Sunday was aimed at resting players ahead of Bayern, this looked more like a dress rehearsal.
Ronaldo, Luka Modric, Toni Kroos, Raphael Varane and Marcelo all returned but there was no place for Gareth Bale, who had also been left out against Malaga. His preserved energy was deemed only valuable enough for 30 minutes off the bench.
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