Neymar brilliantly set up PSG's third goal for Edinson Cavani but later rolled his ankle and was forced off in clear discomfort with around 15 minutes remaining - leaving PSG with 10 men, having just sent on their final substitute Julian Draxler.
Emery told psg.fr: "We showed that this game is special for us and the result was positive - a clear 3-0 win.
"The injury to Neymar was the only black mark. We hope it is nothing serious, we will wait for the scans."
Midfielder Thiago Silva added: "The 'Clasico' is always like this, there is that rivalry. The previous game over there (a 2-2 draw) was not easy but tonight all the players gave their maximum.
"We are happy with the result and to move further ahead in the championship. We finished with 10 because of the injury to Neymar but we still managed to keep control."
OM manager Rudi Garcia was frustrated after what he described as a "strange match".
He told om.net: "We were not at 100 per cent, we were not quite sharp enough. We would have needed PSG to be below their level as well and that was not the case tonight.
"We started well and unfortunately, from their two chances in the first 30 minutes, they scored twice. We made a few defensive errors which cost us a result and we did not produce enough in attack in the first half."
On Neymar, he added: "I hope it's not a big thing. You want to see the top players on the pitch, even if it is against us."
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