Basel, who have one of the league's poorest disciplinary records, suffered defeat against Dinamo on a cold and clear evening at Maksimir.
The match began in controversial circumstances as FC Basel were denied claims by Valentin Stocker for a penalty. Strong centre-back Bostjan Cesar gave GNK Dinamo the lead with a close range header in the 18th minute.
With FC Basel staring at defeat, there was controversy as winger David Degen then had a penalty shout turned down. Basel captain Marco Streller then equalised for FC Basel in the 39th minute with a close range header.
Things turned sour for FC Basel when Degen earned himself an early bath for a vicious foul on 85 minutes. Striker Hilal Soudani then clinched a late winner on 93 minutes with an incisive finish from 9 metres.
Soudani's impact delighted the fans with his late goal.
Player of the Match: Bostjan Cesar (Dinamo)
Attendance: 19,985