The Yorkshire club suspended assistant boss Steve Thompson on Thursday, with no reason given for the decision, leading manager Neil Redfearn to reveal he was considering his position.
Blackburn made the most of the turmoil at Elland Road, but they were helped when Leeds' Rudy Austin was shown a red card for an off-the-ball incident six minutes before the break.
With an extra man, the visitors took control after the break, Tom Cairney volleying home the opener in the 62nd minute before Jordan Rhodes' header doubled the advantage seven minutes later.
Jay Spearing slid in to make it 3-0 with 10 minutes remaining as Blackburn put an end to Leeds' five-match unbeaten run.
Rock-bottom Blackpool were denied a first away win of a miserable season as Eidur Gudjohnsen's 95th-minute equaliser earned Bolton Wanderers a 1-1 draw at the Macron Stadium.
Sergiu Bus returned from injury and stepped off the bench to score his first Sheffield Wednesday goal against Huddersfield Town at Hillsborough.
That looked set to be the winner, only for Ishmael Miller to rescue a 1-1 draw for Huddersfield three minutes later.
It also finished 1-1 between Reading and Cardiff City at the Madejski Stadium - Conor McAleny earning a point for the Welsh side in the 90th minute.
