Giovane Elber stunned the crowd at the Bernabeu stadium into silence last night with a goal which ended the Spanish team's seven-game winning streak at home in this year's competition and left them with a mountain to climb in the second leg next week.
The European champions must now travel to Munich hoping to put an end to another sequence: they have never beaten Bayern Munich at the Olympic Stadium.
Bayern, however, will be without their talismanic midfielder Steffen Effenberg, who was booked for a challenge on Luis Figo in the 78th minute.
Elber, who looked to be in an offside position before he collected the ball, fired in a shot that bounced once in front of Iker Casillas before slipping into the corner of the net.
Bayern owed much to their goalkeeper Oliver Kahn who saved bravely, boldly and sometimes spectacularly from Steve McManaman, Michel Salgado and Raul Gonzalez.
If Bayern found playing in the cauldron of the Bernabeu - where they made their exit in last year's semi-final - intimidating then they were intent on not showing it. Bayern quickly showed how dangerous they can be on the break with Effenberg, Mehmet Scholl and Hasan Salahamidzic combining to take the ball deep into Madrid's half.
Then, in the fifth minute, Effenberg drove a 25-yard free-kick around the Madrid wall and safely into the hands of Casillas.
Ten minutes later another counter-attack saw Salahamidzic float a right-wing cross over Casillas's head. Scholl, left with a narrow angle, shot into the side netting.
As Real slowly got a grip on the ball, and the game, the Scottish referee Hugh Dallas earned the ear-shattering wrath of 74,000 crowd after ignoring appeals for a penalty after Figo tumbled inside the area.
He further increased their rage by calling Figo aside and telling him to save his diving for the swimming pool.
Figo then began to reconfirm his reputation as Europe's most dangerous player. He constantly drifted across from the right to pop up beside McManaman on the left - that was when he was not launching piercing runs through the centre of the Bayern defence.
On one such run, in the 26th minute, he effortlessly shook off the experienced Effenberg and Thomas Linke before shooting from the edge of the box and forcing Kahn into a diving save.
Real Madrid: Casillas; Salgado (Munitis 76), Carlos, Hierro, Helguera, Raul, McManaman, Figo, Guti (Savio 54), Karanka, Makelele. Subs Not Used: Cesar, Campo, Conceicao, Celades, Solari. Booked: Munitis, Hierro.
Bayern Munich: Kahn; Sagnol, Lizarazu, Kuffour, Andersson, Scholl (Sergio 71), Elber (Jancker 73), Effenberg, Jeremies, Salihamidzic, Linke. Subs Not Used: Dreher, Sforza, Tarnat, Hargreaves, Santa Cruz. Booked: Kahn, Effenberg. Goals: Elber 55.
Referee: H Dallas (Scotland).