Lionel Messi sent Fabregas clear five minutes after half-time at an electric Bernabeu stadium enjoying the second "Clasico" of the season and the Spain midfielder finished with ease past Real goalkeeper Diego Lopez.
Barca missed several clear chances to extend their lead before Real centre-back Raphael Varane crowned a fine performance by leaping to head home an equaliser from a Mesut Ozil centre seven minutes from time.
Despite having a slight advantage for the second leg at the Nou Camp at the end of next month, Barca may live to regret not scoring more against a Real team missing regular keeper and captain Iker Casillas and Pepe through injury and the suspended Sergio Ramos.
"These games are always very tough," Fabregas said in an interview with Spanish television broadcaster Canal Plus.
"Considering how the march went the result could have been more favourable from our point of view," added the former Arsenal captain.
"But we will be at home for the return leg in front of our own fans. We are in a good rhythm and having a spectacular season."
In a game pitting a host of Spain team-mates against each other and billed as the latest showdown between Messi and Cristiano Ronaldo, both sides created moments of danger in an ultimately goalless first half.
It was the 223rd meeting between Spain's dominant clubs and their 31st clash in the King's Cup.
Barca knocked Real out in the quarter-finals last season on their way to winning the trophy for a record-extending 26th time and Real beat Barca 1-0 in the 2011 final for their 18th Cup triumph.
Barca went closest to scoring when Xavi curled a 21st-minute free-kick against the crossbar and then had a shot brilliantly cleared off the line by Varane three minutes later.
Ronaldo, captaining the side in his 600th official game, had forced a good save from Barca keeper Jose Manuel Pinto with a free-kick in the second minute and Karim Benzema volleyed narrowly wide just before the half hour.
PERFECT GAME
After Fabregas put Barca ahead, Ronaldo nodded wide with the goal at his mercy before the Portuguese was denied by a superb last-ditch tackle from Gerard Pique.
Fabregas fired just over the bar from a Daniel Alves cross shortly after and then sent Pedro through on goal but his Spain team-mate clipped his shot wide with only Lopez to beat.
Varane's leveller was no more than Real deserved and Lopez, making his debut after joining from Sevilla as cover for Casillas, thrilled the home fans when he palmed away a Jordi Alba strike late on.
Casillas, who broke a bone in his hand this month and is out for up to three months, has not missed a Clasico in more than a decade.
Assistant Real coach Aitor Karanka, standing in for Jose Mourinho, was full of praise for the 19-year-old Varane and Lopez at his post-match news conference.
"Varane played a perfect game, he has his head screwed on just right," Karanka said.
"Diego is a keeper who has played in the top flight for many years and he showed the qualities he has."
The biggest surprise of the night was that neither Messi, who had scored at least once in his last 16 starts for Barca, or Ronaldo were on the scoresheet.
Messi is one goal short of Alfredo di Stefano's record for "Clasico" matches of 18, while Ronaldo's record run of scoring in six straight matches between Real and Barca came to an end.
The winners of the tie will play Atletico Madrid or Sevilla, who meet on Thursday at Atletico's Vicente Calderon stadium, in May's final.
