Komljenović returned to the top division with MSV Duisburg, only missing three games with the Zebras in his two seasons combined, and helping them to two consecutive eighth-place finishes.
FC Kaiserslautern, helping the club qualify to the UEFA Cup in his first season, but being sparingly used in his second, where he played seven times in the team's quarterfinal run in European competition.
After two seasons in the same category with TSV 1860 Munich, Komljenović retired from football at the age of 35, amassing German top flight totals of 210 games and ten goals.
In January 2007, after taking a six-month break, he signed for Union Weißkirchen in Austria (third level) and, in June of the following year, he joined another semi-professional side, VfR Jettingen from Bavaria, competing in Bezirksliga Schwaben-Nord, the eight-tier of German football league system.
Even though he played no part in the 1998 FIFA World Cup qualifying campaign, he was selected by manager Slobodan Santrač for the finals in France, where he would score twice in only three games, against the United States in the group stage (1–0) and against the Netherlands in the round of 16 (1–2 loss).