Brighton took the game to their south coast rivals in the first half, but they could have fallen behind early on.
Svetoslav Todorov, escaping from Paul Merson's quickly taken free-kick, had appeals for a penalty turned down as he tried to round Ben Roberts, making his debut in the Brighton goal on a month's loan from Charlton.
Bobby Zamora spurned a good opportunity to put the home side in front, firing just wide from close range after Paul Brooker set him up.
Roberts made a fine save to stop Nigel Quashie giving Portsmouth the lead against the run of play on the stroke of half time, smothering his shot at the expense of a corner.
Quashie almost broke the deadlock five minutes into the second half, but his left-foot drive from 25 yards hit the base of the post with Roberts beaten.
A superbly taken goal by Zamora gave Brighton the advantage their enterprise deserved.
The Portsmouth defence failed to deal with a bouncing ball midway inside their own half and Brooker's lobbed pass put Zamora into space and he cut inside two defenders to slot his seventh of the season and first for seven games.
That galvanised a subdued Portsmouth into action. They brought on new Nigerian striker Yakubu Ayegbeni and it took a fine one handed save from Roberts to stop him from equalising.
The let off was short lived for Brighton as Todorov turned on Quashie's pass to strike his 13th goal of the season from just inside the area.
Lassina Diabate could have given Portsmouth all three points, but he headed wide from Ayegbeni's cross.
Brighton boss Steve Coppell moaned: "You cannot afford to give a side of Portsmouth's quality room to play and we did well to close them down.
"It was a tight match and probably a fair result, although we are disappointed not to have taken all three points.
"We have played well this week, but have collected only a point from two league games at Coventry and were knocked out of the FA Cup at Norwich.
"I don't feel as if we have got our just rewards.
"Bobby Zamora has never hidden, even though he hasn't been scoring goals recently, and I thought Ben Roberts did very well. He only met the players for the first time yesterday and spent last night looking at the programme to familiarise himself with their names and faces."Portsmouth manager Harry Redknapp said: "It reminded me of a third round FA Cup tie and it was a fair result.
"Brighton didn't give us any time or space to play. They worked hard but we came back like we always have done this season when we have gone behind."