Leeds will take a 2-1 lead to Germany but a last-minute 1860 Munich goal and two red cards puts their Champions League progress in some doubt.
Leeds were strolling to a comfortable victory as they led 2-0 with 15 minutes to go and a man advantage but then referee Costas Kapitanis took centre stage.
The Cypriot official had already sent off 1860 Munich's Ned Zelic for violent conduct - even though he appeared not to have made contact with Ian Harte - and handed out a number of cautions.
But as Leeds tried to seal the game, the referee showed harsh second yellow cards to Olivier Dacourt and Eirik Bakke, leaving the Elland Road side needing to play the last six minutes plus four minutes of injury time a man down.
Devastated
Leeds boss David O'Leary, already robbed of seven first-team players through injury, was devastated to lose Dacourt and Bakke, who will be suspended, for the second leg.
"I don't mean this as a joke, but I don't know what side I can field for that game," O'Leary said.
"I don't know whether I've got seven players for the bench given that I've now two more midfielders out to add to the list of long-term injuries.
"The only fit midfield player I will have for the game is Lee Bowyer because
I really don't see anybody making a comeback from injury in time."
Fury
And O'Leary had to bite his tongue when asked about the referee's performance, but his feelings were clear.
"I thought all the sendings off were wrong. I thought they were a joke, unbelievable," he said.
"For Olivier and Eirik I don't think they should have been booked first time round and that's the bottom line."
Leeds had taken the lead after 39 minutes when Martin Stranzl tried to play the ball back to his own keeper but Alan Smith nipped in front to score. Two minutes later 1860 Munich were down to 10 men as Zelic was sent off.
The referee gave Leeds the chance to make the score 2-0 after 71 minutes from the penalty spot when Smith was tripped, even though contact was minimal and appeared to be outside the box.
Home and dry
Ian Harte converted the spot-kick and Leeds looked home and dry, but Dacourt received a second yellow card for diving four minutes later and Bakke followed him picking up his second booking when he challenged for a high ball.
1860 Munich then piled on the pressure in the closing stages and Agostino's header gave Nigel Martyn no chance and Leeds plenty of headaches for the second leg.
A disappointed O'Leary said: "I'm not very confident about going through.
"I'm not being defeatist, I'm just being realistic, it's no way to be going into the biggest game this club has had without nine players."
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