Fernando Torres put Liverpool ahead before Javier Mascherano was ruled to have fouled Valencia, and Wayne Rooney fired in a rebound from his spot-kick.
"The way he fell down is strange. When you see the replay it is suspicious how he went to the ground," said Benitez.
Ji-Sung Park headed in the winner for United in the 60th minute.
The result returned United to the top of the Premier League and damaged Liverpool's hopes of securing fourth place in the table and the final Champions League spot.
Benitez believes the penalty was the turning point of the match.
"We gave away the penalty too early - but there are doubts about the penalty," said Benitez.
Asked whether he thought Valencia had dived, he added: "From the replay I think so.
"The penalty made a big difference. We were playing well and had confidence and then one situation changed everything."
There was also some doubt as to whether referee Howard Webb should have awarded a free-kick instead of a penalty as the initial contact between Mascherano and Valencia appeared to take place outside the area.
But Manchester United boss Sir Alex Ferguson was adamant that Webb made the right decision, although he did question the fact that Mascherano was not sent off.
"The referee was right, he tugged him down. He didn't bring him down outside the box, he didn't go down until he was inside the box. The decision was correct," said Ferguson.
"I thought it was a red card. There was no way Jamie Carragher could get across and stop Valencia from shooting - he is too quick for Carragher to get across.
"The law is if you stop someone from having a goalscoring opportunity it is a red card. Not today."
Benitez disagreed with Ferguson - as he did during the match when the pair clashed on the touchline.
"Jamie Carragher was coming inside so he was in the middle of the action [so Mascherano should not have been red-carded]," said the Reds boss.
And of their touchline exchange, Benitez said: "When you have different opinions you have to express them. He [Ferguson] has his own opinion about everything."
Despite his grievances about the penalty, Benitez did not feel Webb was affected by Ferguson's pre-match suggestion that Liverpool benefit from many refereeing decisions that other sides do not.
"Some decisions in the past have not been the best for us but I consider Howard Webb a good referee," Benitez added.
"The referees are professional. We know the influence of Sir Alex in everything but he is a good referee."
The Spaniard also tried to put a brave face on the defeat.
"It was a tight game and we had a good chance with Fernando or Yossi [Benayoun] late on," he added.
"They (United) didn't create too many chances but they were always dangerous. It was close but the little things make a difference."
Source: BBC Sport
Source: BBC Sport