Leon Knight stepped up to the spot and after a staggered run up, neatly placed the ball into Jonathan Brain's top right.
Vale had the chance to equalise on two occasions soon after but a combination of Ben Roberts and poor finishing kept Brighton ahead. Steve Brooker struck an effort from the edge of the box but Roberts parried well and Billy Paynter hould have done better when he headed just over from ten yards.
Paynter made no mistake with his second chance in the 26th minute when Mark Bridge-Wilkinson's free kick after a late tackle on Brooker was met by the young forward in the centre of the box and redirected past Roberts.
The second half continued in the way the first had left off with Port Vale claiming the Lions share of play. Both sides made changes but their frustrations continued with neither defence willing to give in easily.
The home side were hard done by in the 70th minute when defender Sam Collins was held down in the area to herald valid calls for a penalty. However, referee Kevin Friend saw no infringement and allowed play to continue.
The Valiants had a final chance late on but Steve McPhee's shot was scuffed giving Roberts an easy save. Port Vale assistant manager Dean Glover said: "We've come from one down and wanted to get at them again but they put men behind the ball and defended really well.
"There's 12 games left and it is in our own hands to do something this season."