The knockout stage of the 1999–2000 UEFA Champions League began on 4 April 2000 and ended with the final at the Stade de France in Saint-Denis on 24 May 2000.
If the two teams scored the same number of goals over the two legs, the team that scored more goals away from home qualified for the next round; if both teams scored the same number of away goals, matches would go to golden goal extra time and then penalties if the teams could not be separated after extra time.
Bayern Munich won 3–2 on aggregate.
Real Madrid won 3–2 on aggregate.
Real Madrid won 3–2 on aggregate.