Two-time world player of the year Lionel Messi came on midway through the second-half to add another two, his first a header set up by a Fabregas cross to give last season’s beaten finalists a healthy advantage ahead of next week’s second leg.
Fabregas – who has been an instant success at the Spanish and European champions since his dream move from Arsenal last summer – struck twice in the opening 20 minutes.
The second was the pick of them as he produced a sublime lob from a fine pass by Xavi – who had also set him up for the opener.
On Tuesday holders Real Madrid had had to dig deep to come from two goals down and beat heavily-bankrolled Malaga 3-2.
Malaga – who have been transformed since Qatari Sheikh Abdullah Al Thani invested in them – were looking comfortable after goals by Sergio Sanchez and Martin de Michelis put them ahead but Real roused themselves to gain a slight advantage ahead of the second leg in Malaga next week.
Three goals in 10 minutes in the second-half by German midfielder Sami Khedira, Argentinian striker Gonzalo Higuain and French strike partner Karim Benzema saw a first choice Real side edge to victory.
Both Malaga’s goals came from headers before the half hour mark but the hosts fortunes were transformed when coach Jose Mourinho sent on Khedira, Mesut Ozil and Benzema at half-time.
Khedira reduced the deficit after surging through the defence and lofting the ball into the net in the 68th minute and Higuain took advantage of a defensive mix-up by levelling two minutes later.
The comeback was complete when Higuain found Benzema with a superb defence splitting pass in the 78th minute and the rejuvenated French international made no mistake.
Real could have extended their lead on several occasions after that, Cristiano Ronaldo scoring with the last kick of the match – a spectacular bicycle kick – but it was ruled out rightly for offside.