Goals from Filip Djordjevic, Aleksandar Kolarov and Lazar Markovic put the game well beyond the hosts, who never looked like avenging the 6-1 mauling they suffered at the hands of the same opponents in Novi Sad a year ago.
Gareth Bale, a pre-match doubt due to a groin problem, appeared just before the hour to get his first action since joining Real Madrid for £86m. He almost scored a wonderful late free-kick, which was about as good as it got for the hosts.
Chris Coleman has stressed the importance of finishing third in this group in order to secure a better seeding for Euro 2016 qualification, but Scotland's win in Macedonia sent Wales plunging to the bottom of the section on goal difference, and they were booed off at full-time.
Kolarov whipped in an early cross from the left, which Filip Djuricic headed straight at Boaz Myhill, but Djordjevic headed in the rebound with no Wales defender in sight.
Aaron Ramsey, the hosts' captain, was the best player on the pitch by some distance, and his link-ups with Craig Bellamy proved Wales' best attacking outlet.
They were soon on the defensive again, though, as another Crofts error gave Ljubomir Fejsa a sight of goal only for Myhill to save, but the goalkeeper then stood no chance when Kolarov deposited an unstoppable drive into the top corner to double the visitors' lead.
Welsh woes were compounded when an overworked Myhill superbly saved Kolarov's shot, no-one reacting quickly enough to prevent Markovic putting away the rebound.
Boos rang out around the Cardiff City Stadium and Coleman, perhaps sensing the mood, quickly readied Bale, who came on in place of Andy King for his first action since becoming the world's most expensive player.
He quickly had two shots on goal, with Vladimir Stojkovic beating away one fierce drive and Bale putting the rebound wide. During a meandering final quarter he was the only real point of interest. One lovely, balanced run was halted as he went down, and was ordered to his feet by the referee.
Bale then almost scored with a swerving and dipping free-kick which Stojkovic just about tipped over.