The former Arsenal captain, who signed on Monday for around £35m, came on as an 82nd-minute substitute after Karim Benzema looked to have sent the tie into extra time by levelling the game at 4-4.
But minutes after he appeared, Lionel Messi hit a late winner – his second goal – to make it 3-2 on the night.
Real’s Marcelo was sent off at the end.
The Brazilian full-back was given a straight red card for hacking at Fabregas in injury time, an incident which led to an ugly melee on the sidelines before the full-time whistle was blown.
Barcelona, who had never before beaten Real on aggregate in a Spanish Super Cup, started the match with the same starting XI that defeated Manchester United in the Champions League final in May.