The Premier League side recovered from the loss of an early Ezequiel Lavezzi goal to equalise courtesy of an Eden Hazard penalty just before the half-hour mark and the Belgian also struck the post before half-time.
However, PSG seized the initiative again in the second period and a David Luiz own goal put them back in front before Javier Pastore's stoppage-time effort handed the Ligue 1 leaders a potentially decisive two-goal advantage heading into next Tuesday's return at Stamford Bridge.
"I think from a strategic point of view, the team had great discipline,” said Mourhinho. “And they did the most difficult things to do in the game very well.
"However, we couldn't transform the half-chances that we created into goals and on top of that we made defensive mistakes, individual defensive mistakes. So we paid the price."
Meanwhile, PSG coach Laurent Blanc singled out Lavezzi for praise after the Argentinian produced an outstanding performance and also lauded his team for their second-half display.
"Ezequiel is back on top form now and he brings us depth and pace in attack,” said Blanc.
“The performance was encouraging. We had a very constructive discussion at half-time, we knew we had to work harder and be more disciplined in midfield, and the second half was excellent."
Ronaldo injury no worry for Ancelotti
Real Madrid coach Carlo Ancelotti insisted he was not concerned by an injury that forced Cristiano Ronaldo to be withdrawn 10 minutes from time as his side edged towards the Champions League semi-finals with a 3-0 win over Borussia Dortmund on Wednesday.
The Portuguese scored a record-equalling 14th Champions League goal of the season to all but seal Real's place in the last four after first-half strikes from Gareth Bale and Isco had put Los Blancos in command.
However, uncharacteristically, Ronaldo did not finish the 90 minutes as he was forced off by a minor knee injury that has bothered him for the last couple of weeks.
"We will wait and see what the problem is, but at the moment we are not worried,” said Italian Ancelotti, suggesting Ronaldo will start Saturday's crucial La Liga visit to Real Sociedad. “We are not thinking about giving him a rest,"
On the other hand, Dortmund boss Jurgen Klopp was left to rue his side's inability to take their opportunities as they created plenty of openings after the break, but too often took the wrong option with their final ball.
"There are many things we can learn,” said Klopp. “You have to do the right tactical things against the best teams in the world so that they can't do what they want. That was the problem tonight [Wednesday].”
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