The knockout stage of the 1998–99 UEFA Champions League began on 3 March 1999, and ended with the final at the Camp Nou in Barcelona, Spain, on 26 May 1999.
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.
Dynamo Kyiv won 3–1 on aggregate.
Bayern Munich won 4–3 on aggregate.
The final was played on 26 May 1999 at the Camp Nou in Barcelona, Spain.