Goals from Ryan Fraser and Fabian Schar in the space of two first-half minutes was enough to see the Magpies extend their unbeaten run in the Premier League to eight games.
The Toon were made to work for the result, though, as a bullet header from Seagulls captain Lewis Dunk gave the visitors a lifeline.
However, there was no comeback for Graham Potter's side this time as they succumbed to a fourth straight defeat in the league.
The result leaves Brighton in 13th place, five points above Newcastle who sit a place behind them in 12th and with a game in hand.
As has often been the case this season, Brighton will be disappointed not to have taken their chances when on top.
In the early exchanges they controlled possession and had most of the ball in Newcastle's territory.
They will be even more disappointed when the goals they conceded were via a counter-attack and a set-piece.
After Marc Cucurella lost the ball in Newcastle's half, the ball broke to Chris Wood who did very well to see the run of Jacob Murphy.
A fine pass from the striker enabled the winger to sprint away from the defence.
His effort saw the ball go over Robert Sanchez, but unfortunately strike the left post.
Thankfully for him, and the majority of the fans inside St James' Park, Ryan Fraser was on hand to smash the ball in from close-range.
Moments later, the Toon Army were in dreamland as a superb delivery from Fraser on the right hand side gave the hosts a two goal advantage.
Schar met the cross, and his header found the net inside of the near post.
Brighton goalkeeper Sanchez, though, would have been disappointed to let the goal in as he got a strong hand onto the ball.
It could have also gotten worse for the visitors when a slip by a Brighton defender inside the penalty area was not capitalised by Murphy, who could only send his shot straight to the goalkeeper.
Whatever was said at half-time by Potter though clearly worked as Brighton brought the contest back to life.
An in swinging corner from Pascal Gross was met by Dunk who rose above the crowd to head the ball in from close range.
For the remainder of the half, the Seagulls threatened to bring the score line back on level terms, but Howe's players stood firm and held out for a valuable three points.