Fulham ran out comfortable winners at St James's Park thanks to two goals from Ryan Sessegnon and a strike from Tom Cairney.
Daryl Murphy scored a consolation goal for United after coming off the bench.
Newcastle lead the Championship by goal difference ahead of Saturday's game against Birmingham City at St Andrew's.
“We knew it could be a difficult game, and we knew we had to do well at the beginning and not make mistakes," said United manager Benitez, who was appointed a year ago.
"But we started making mistakes, and we paid for that. Fulham are a good team – they passed the ball well and they have pace. We were giving the ball away, and that was giving them the chance to play in the way that they like to play.
“When you have tried and have made mistakes, you have to analyse why. It is not as though the players were not trying in terms of effort.
"Sometimes, it is just the wrong decision, and that is something we have to improve. In terms of effort, you could see we were running and working very hard."
Benitez revealed that defender Ciaran Clark was forced off the pitch with a knee problem.
“Clark picked up a knock with his knee, so we will have to see how he is," said Benitez.
Meanwhile, Fulham Slavisa Jokanovic hailed his "clinical" team after the match.
"We played very good football today," said Jokanovic. "We tried to win the game. Our style, we move the ball, we had control.
"We were more clinical. I believe at the end my team deserved the result. It's a great step for us, everything is open, some teams have more points than what we have right now."