Edinson Cavani and Angel Di Maria scored either side of half-time to record an eighth successive league victory for the champions, moving three points clear of Monaco, who have two games in hand.
Emery praised the visitors for their attacking spirit after an entertaining game at the Parc des Princes that keeps PSG in the title chase.
"We were happy for the three points, the spectators saw a good game," Emery told Canal+.
"Montpellier came to play the attack and make the draw and we deserved to win the game.
"Many things happened in 90 minutes, both for us and for Montpellier, but I think the victory is correct."
Javier Pastore was replaced by Julian Draxler with nine minutes to go and Emery said the midfielder had suffered a muscle injury, while revealing the reason for Adrien Rabiot's absence.
"Pastore, it is a small muscular pain," Emery said. We will get the analysis of the doctor tomorrow. But maybe he has a small muscle injury, in the thigh.
"[Rabiot's injury is] a blow. We will wait and it depends on how he reacts. It will improve for Wednesday's game but it was not possible for today.
"We will wait tomorrow. Monday, we will have training in the afternoon. I hope it will be well in the afternoon but we will know later."