Mayhem erupted after he was fouled by Madrid left-back Marcelo. The Brazilian was sent off as every player and most of the backroom staffs piled in.
Ex-Arsenal midfielder Fabregas was treated by medical staff but was fit enough to come back on for the last minutes. By then the referee had also red-carded Barcelona's David Villa and Madrid's Mesut Ozil.
Jose Mourinho's Madrid were beaten 3-2 on the night to slump to an aggregate 5-4 defeat.
Leo Messi hit the late winner.
Messi put Barca 2-1 up before Karim Benzema levelled again.