The 1999 UEFA Intertoto Cup finals were won by Montpellier, Juventus, and West Ham United.

2–2 on aggregate, Rudar Velenje won on away goals rule.

Ceahlăul Piatra Neamţ won 2–0 on aggregate.

2–2 on aggregate, Qarabağ won on away goals rule.

Ceahlăul Piatra Neamţ won 5–2 on aggregate.

1–1 on aggregate, Juventus won on away goals rule.

The game was abandoned in the 114th minute of extra time due to some objects being thrown on the pitch, some even hitting the referee.

UEFA banned Perugia and awarded a 3–0 win to Trabzonspor.

West Ham United won 2–1 on aggregate.

2–2 on aggregate, Rennes won on away goals rule.

3–3 on aggregate, Hamburg won on away goals rule.

West Ham United won 2–0 on aggregate.