The Blues boss rushed to the corner of the pitch to his players, who were celebrating Demba Ba's late strike, but says he was passing on tactical instructions.
The Senegalese striker prodded home late to send the Blues through to the semifinals of the Champions League, with Mourinho's men advancing on away goals after a 3-3 aggregate draw with the Ligue 1 side.
The goal, which made it 2-0 on the night after Andre Schurrle had struck in the first half, prompted Mourinho to charge down the sideline, reminiscent of his wild celebrations at Old Trafford with Porto back in 2004, but the 51-year-old says he was passing on tactical instructions.
When asked if he ran down the sideline to celebrate Ba's goal, he told ITV Sport: "No, not to celebrate. To tell Fernando [Torres] and Demba the changes we had to do. Because there was still three minutes plus extra time and playing the way we were playing was too risky. I wanted Demba to play in front of the defenders and I wanted Fernando to defend Maxwell.
"We did enough in the beginning of the second half to score before but we couldn't. After that there was a contradiction of what they are and what they were saying yesterday that they wanted to do. They played counterattack, closing everything and it was difficult for us to penetrate in the second part of the second half."
Mourinho believed that Chelsea deserved to advance to the last four, insisting that Laurent Blanc's defensive tactics proved to be his undoing. He added: "Demba made a crucial finish for us and I think we deserved it. The team that decided to defend was punished and the team that gave everything with the heart deserved to go through to the semis."