The two forwards appeared to have a disagreement over who would take a penalty in the 79th minute of Sunday's Ligue 1 clash against Lyon, before Cavani stepped forward and had his effort saved.
PSG still went on to win 2-0 on home soil, but Emery is keen to avoid an issue when it comes to two of his star players squabbling over penalty duties.
"I have told them to sort it out between themselves. I think that they are capable of doing that and that they will both be our kickers," Emery told reporters. "If they cannot reach an agreement, I will decide for them. I do not want this to become a problem for us."
PSG have won all six of their Ligue 1 fixtures this season to sit atop the table on 18 points.