Tomer Hemed struck six minutes into the second half to clinch the points for Brighton, but replays showed Lewis Dunk and Bruno blocking off Newcastle players in the build-up - even if there was no appeal at the time.
Benitez's side had won their previous three Premier League games and he was disappointed that they could not maintain their unbeaten run.
"I think that we did enough to get a point at least," he told Sky Sports. "We had some chances, they had some chances. We had a lot of control and some chances at the end.
"And the goal, for me, was a foul. There is pushing, blocking players, and it's so clear. But we cannot change the decision. Normally, we do not get [those decisions]."
On his mood after a rare defeat, Benitez added to BBC Sport: "I was happy before the game and not so happy after the game. It is a long way to go so we have to keep going and keep improving."
Chris Hughton acknowledged that Brighton were far from clear winners against his former club, identifying their clean sheet as vital to the victory.
"It was a hard-fought victory," he said. "They're a good side, Newcastle, as they've shown in the last few games.
"There wasn't much between the two teams. Sometimes when you're the home team, you just get a little bit more in your favour. The one opportunity, we took.
"But it was a tight game and we had to dig deep at times. The clean sheet [was key].
"We didn't feel like there were going to be a lot of chances, so we had to make sure - against a very good Newcastle team - to keep a clean sheet and look for those moments."
2 - Brighton have won back-to-back home league games in the top-flight for the first time since November 1982. Flying. — OptaJoe (@OptaJoe) September 24, 2017
Hemed trod on DeAndre Yedlin in a late flashpoint but, after the goalscorer had protested his innocence, Hughton suggested any collision was unintentional.
"There is no doubt that there's been some contact - we can see that - but my first impression is that there's no intent," he added. "And knowing the individual, I would say there's no intent."