 He had his best moments in Maribor during the 1999–2000 season, when he led the team through qualifications for the elite UEFA Champions League where the team eventually qualified and played in.Balajić scored an important goal in the second leg of the third qualifying round against Olympique Lyonnais, which was won by Maribor 3–0 on aggregate.He then played for the team in group stages and scored one of two Maribor goals in the process, against FC Dynamo Kyiv.