The 1998–99 UEFA Cup was won by Parma in the final against Marseille.

The labels in the parentheses show how each team qualified for the place of its starting round:[1] Argeş Piteşti won 7–1 on aggregate.

Inter Bratislava won 4–0 on aggregate.

3–3 on aggregate; Zalgiris Vilnius won on away goals.

Hapoel Tel Aviv won 6–2 on aggregate.

Shakhtar Donetsk won 6–1 on aggregate.

IFK Göteborg won 7–0 on aggregate.

Red Star Belgrade won 11–0 on aggregate.

Red Star Belgrade won 4–2 on aggregate.

3–3 on aggregate; Rapid Wien won on away goals.

4–4 on aggregate; Argeş Piteşti won on away goals.

1–1 on aggregate; Slavia Prague won 5–4 on penalties.

2–2 on aggregate; CSKA Sofia won on away goals.

3–3 on aggregate; Red Star Belgrade won 4–3 on penalties.

Celta de Vigo won 8–0 on aggregate.

1–1 on aggregate; Leeds United won 4–1 on penalties.

The match was abandoned at half-time after the fourth official, Philippe Flament of Belgium, sustained a knee injury and bruising from a firecracker thrown onto the pitch by fans in the stands.

At the moment of the incident, Fiorentina led 2–1 on the night and 4-1 on aggregate.

Four days later at a UEFA emergency meeting, Fiorentina was kicked out of the UEFA Cup and the match was recorded as a 0–3 Grasshopper win.

Future expulsion from European competition for Fiorentina was also considered by UEFA but eventually ruled out because of mitigating circumstances, specifically that the match, as part of an earlier punishment, was not played at Fiorentina's home stadium but in Salerno and credible evidence that the firecracker was likely thrown by fans of the local club Salernitana holding a grudge following a recent Serie A fixture between the two clubs.

Celta de Vigo won 3–2 on aggregate.

Celta de Vigo won 4–1 on aggregate.