The Blues took the lead completely against the run of play in the first half but had Didier Drogba controversially sent off in the 55th minute and conceded two goals in the last quarter of the game.
Mourinho caused a major surprise just before kick-off by naming Damien Duff in his starting line-up after previously saying the Republic of Ireland international would miss the match with a knee injury.
William Gallas also started after recovering from the groin strain he sustained in Sunday's FA Cup fifth round defeat at Newcastle United.
Chelsea started the match poorly though and Ronaldinho fired a third minute shot just wide before Samuel Eto'o also went close to giving the Catalan giants the lead.
In the tenth minute Ronaldinho fired narrowly wide from Ludovic Giuly's cross as Barca continued to dominate.
On the quarter-hour, Drogba was booked for a foul on Rafael Marquez but Chelsea slowly started to quell the early Barcelona pressure.
However, it was still a shock when the Premiership leaders took the lead in the 33rd minute. Frank Lampard played in Duff who beat Giovanni van Bronckhorst before crossing for Joe Cole. Juliano Belletti got to the ball first but could only turn it into his own net from six yards out.
Drogba fired wide with only goalkeeper Victor Valdes to beat two minutes later and Cole also went close before the break as the hosts suddenly looked rattled.
The home fans were starting to get frustrated when the match turned on a 55th minute incident.
Referee Anders Frisk decided to send Drogba off after the Ivory Coast international challenged for a 50-50 ball with Valdes.
It was a controversial dismissal and set up some frantic Barcelona attacking. Substitute Andres Iniesta sent a left-foot shot inches wide of the post after Ricardo Carvalho had managed to block an initial shot from Eto'o.
Another substitute Maxi Lopez finally equalised in the 67th minute when he beat Gallas before firing a right-foot shot beyond Petr Cech after good interplay between Ronaldinho and Eto'o.
Seven minutes later Cameroon international Eto'o made it 2-1 when he reacted quickest to beat Cech after Lopez had mishit his shot towards goal.
Barca swarmed forward in search of a crucial third goal but Cech remained defiant making a string of fine saves while Eto'o went close to scoring his second goal of the evening.
But a third goal would not come, leaving the tie evenly poised for next month's second leg at Stamford Bridge.