Ajax opened the scoring in the 28th minute through Danish forward Lucas Andersen, only for APOEL's Brazilian midfielder Gustavo Manduca to level from the penalty spot three minutes later.
Gerard Pique headed home the only goal of the game from Lionel Messi's free-kick midway through the first-half, but APOEL managed to subdue a much-changed Barca side despite the presence of Messi and Neymar up front.
Barcelona coach Luis Enrique has also included Brazilian back Douglas for the first time since his signing for the Champions League game against APOEL Nicosia.
Barcelona's run of six consecutive Champions League semi-finals was ended by a quarter-final exit to Atletico Madrid last season, but after starting his reign with three consecutive wins in La Liga, coach Luis Enrique refused to make any minimum requirement of his star-studded squad for this campaign.
Lionel Messi and Neymar have been in superb form for Barcelona F.C. in La Liga. The club will hope the magic continues in the Champions League as well.
Nine-time champions Real Madrid qualified for the Champions League semi-finals here on Wednesday, beating APOEL Nicosia 5-2 in their quarter-final second-leg clash and by 8-2 on aggregate.
Real Madrid go into the second leg of their Champions League quarter-final against APOEL Nicosia on Wednesday knowing that the hard work has already been done, but full of respect for their opponents according to Brazilian full-back Marcelo.
Cypriot minnows APOEL put on a brave face following the Champion League quarter final draw on Friday, saying they were "proud" to come up against Spanish giants Real Madrid.
Spanish giants Barcelona and Real Madrid were kept apart in the draw for the Champions League quarter- and semi-finals here on Friday, setting up the possibility of a final showdown between the two in Munich.