Asked if the defeat was deserved, Benitez said to ITV1: "It's difficult to say, both sides had chances.
"The penalty was a crucial decision. I think we can talk about this for one hour, there were too many things I didn't like but I can't change those things now and we have to accept the situation."
Asked if he was blaming Dowd, Benitez repeated: "There are too many things to talk about. I could see a lot of things I didn't like but you cannot change the result so we have to move forward."
Asked specifically about whether the penalty decision was right or wrong, he said: "Again I would say it depends on your point of view, but too many things I didn't like."
Benitez revealed Fernando Torres and Steven Gerrard - both withdrawn early with injuries - will undergo scans on Thursday.
Caretaker Reading boss Brian McDermott was understandably delighted but reluctant to consider how the win may affect his long-term job prospects.
"I thought our guys were terrific tonight, it was a really good performance and I thought we were unfortunate to go in 1-0 down," he said.
"You always think you're going to have a chance and I thought we were good value tonight."
McDermott hailed hero Long on ITV, adding: "He's a great lad, I'm so pleased for him tonight.
"They were all terrific tonight but I'm so pleased that Shane got the goal, I'm chuffed for him."
Asked about his new 'bargaining power' in terms of making his role permanent, McDermott insisted he would not be going straight to talk to chairman John Madejski on Wednesday night.
"He (Madejski) is just well pleased and he's coming back on the bus with us tonight."