The pair became involved in an on-pitch spat during the side's 2-0 win over Lyon earlier this month as they bickered over who should take a spot kick.
The row is said to have escalated after the game, with rumours suggesting that the pair had to be kept apart in the dressing room afterwards and that world-record signing Neymar subsequently demanded that Cavani be sold.
At the time Emery admitted that he had ask the players to sort out the issue themselves, but now he has declared that he has "told them how things will work".
"Many of our players are capable [of taking penalties]," Emery told reporters ahead of the club's Champions League game with Bayern Munich. "Many of them also want to.
"Edinson and Neymar are ready. There will be plenty of penalties and both will benefit from that. I have spoken with both of them. I have told them how things will work from here."
PSG have also denied reports that Cavani turned down a €1m (£880,000) offer from the club to relinquish his penalty-taking role.