The Seagulls stretched their unbeaten league record in 2012 to 12 games against Portsmouth although a bore draw looked to be on the cards before Vicente was introduced midway through the second half.
The former Valencia winger forced a fine save from Pompey goalkeeper Jamie Ashdown before his free-kick found the bottom corner.
Vicente then put the game to bed in injury time with a low finish after being teed up by fellow substitute Kazenga LuaLua.
Beleaguered Portsmouth overcame a nervous start and had several first-half chances but they were forced to defend for large spells in the second half and the pressure eventually told.
The visitors have lost their last three matches and remain bottom of the Championship, eight points adrift of safety.
Will Buckley, Craig Noone and Sam Vokes all returned to Brighton's starting line-up, with Gai Assulin, Abdul Razak and Craig Mackail-Smith making way.
Portsmouth boss Michael Appleton also made three changes to his line-up as Ashdown, Tal Ben Haim and Marko Futacs replaced Stephen Henderson, Aaron Mokoena and Hayden Mullins.
The visitors, bottom of the Championship after being deducted 10 points last month for going into administration, were firmly on the back foot in the early stages.
Yet, they were the first to have a real sniff at goal as Luke Varney curled narrowly wide of the right-hand post from 25 yards.
Scott Allan then made some room for himself just outside the area before his rasping drive was tipped round the post by Seagulls goalkeeper Peter Brezovan.
The visitors were starting to grow in stature as the half wore on and Allan's decent delivery from a corner somehow managed to evade everyone.
The midfielder then narrowly lobbed over from just outside the box after a poor clearance from Gordon Greer.
But on the stroke of half-time, the hosts nearly took an undeserved lead as an almighty scramble in Portsmouth's penalty box created by Alan Navarro's long-range shot ended with Vokes being denied by Ashdown from close range.
After a relatively quiet 45 minutes, the second half began in much the same way, with neither side able to stamp their authority on the clash.
However, Brighton right-back Joe Mattock's volley from Buckley's cross produced a marvellous save from Ashdown before Pompey cleared their lines to ensure the score remained goalless.
Seagulls manager Gus Poyet introduced former Spain international Vicente for Noone in an effort to break the deadlock.
And the replacement almost had an immediate impact as, after Ashley Barnes's strike was blocked by Ben Haim, Vicente's follow-up was saved by Ashdown.
The 30-year-old was not to be denied, though, and his strike put Brighton well on their way to three points.
After David Norris had fouled Vicente on the edge of the area, the winger picked himself up before drilling past Ashdown in the 75th minute.
Portsmouth did push forward in an attempt to force an equaliser but their failure to test Brezovan was telling and their misery was compounded in injury time.
LuaLua picked out Vicente from the left by-line and he made no mistake from close range.
