Graham Potter’s men had 68% possession but goals from Ryan Fraser and Fabian Schar inside the opening 15 minutes clinched victory.
United, at times, were hanging on after Lewis Dunk made it 2-1 on 55 minutes but the hosts put their bodies on the line to see out a big three points.
Fraser was one of the players who looked to be carrying an injury but Howe hopes the in-form Scot will be OK ahead of facing Southampton on Thursday night.
“I don’t know,” Howe said when asked if Fraser was OK after gingerly walking off when he was substituted for Bruno Guimaraes on 79 minutes. “I’ll have to speak to him.
“I think there are a few boys in the dressing room that are nursing little things today.
“You saw a few of them stretching on the pitch. It must have been a big, physical effort for us, so there were a few players right on the edge.
“Hopefully Ryan will be OK but I don’t know.”
Despite sitting in 14th with a healthy gap over the bottom three, Howe insists Newcastle remain in a relegation battle.
“In terms of result, it’s absolutely fantastic for us,” Howe said. “We said pre-game nothing has changed and that we are still in a relegation fight. We still are.
“I have a lot of respect for Brighton. They are a tough opponent. We knew we would be tactically tested.
“We showed mental toughness, especially at 2-1. When they scored the game was very much in the balance but we handled it well. We defended well and put our bodies on the line and did the nasty stuff really well.
“We have got a lot of work to do to be where we want to be. I am very realistic and I know how quickly football can change.”