Luiz was deployed in midfield in a 3-5-2 system in N'Golo Kante's absence but was taken off with a calf problem in the second half.
While Conte insisted that Luiz's injury is not serious, the Italian stressed that he cannot risk losing him for a long period due to the lack of options in the Blues squad.
"It was fair. It was a difficult game against a good team," Conte told BT Sport. "Above all in the first half we suffered, our performance was good but for sure our football is different than today.
"We suffered possession and it wasn't easy in the first half, despite scoring two goals. The change of the system wasn't good, but when you are in a difficult situation you have to change and sometimes to improvise.
"When we changed in the second half the situation was changing. David Luiz had a little problem in his calf and in this moment I can't risk my players. We are playing always the same players. It's difficult to risk losing him or other players for many times."
The result keeps Chelsea top of Group C with seven points from three games.