The Chelsea winger was sent from the pitch in the 80th minute of his side's 0-0 draw with Swansea City (2-0 aggregate loss) for kicking the ball from under the youth as he lay on top of it behind the goal-line.
Replays show there was some force from Hazard in trying to retrieve the ball, a matter which will be dealt with by the Football Association, but Benitez insists the pair have exchanged pleasantries since the end of the match in a bid to smooth things over.
"Eden Hazard has been in to see the ballboy and the two have apologised to each other," the Spaniard said.
"The ballboy knows he was wasting time. We are disappointed to lose the player but we cannot change things. They both recognise there was a mistake.
"The boy was apologising for time wasting. Hazard was frustrated and tried to get the ball. He was kicking the ball and getting the ball.
"We can analyse if for half an hour but we know that both are wrong."