Substitute Yann Kermorgant fired the Cherries to their fifth league win on the spin after Lewis Dunk had fouled Callum Wilson in the box in the 75th minute.
The French striker’s penalty came after Sam Baldock looked to have grabbed a point for the Seagulls with his first goal since signing from Bristol City.
Sami Hyypia’s men, who had twice got themselves back in the game after going behind, remain just above the relegation spots after one win from 12 league matches.
The visitors started strongest in blustery conditions with a Gary Gardner free-kick being deflected just past a post.
Eddie Howe’s Cherries were making uncharacteristically sloppy passes in possession but did force the first real chance after 15 minutes.
Matt Ritchie jinked his way into the box and forced a low save from Ali Al-Habsi, who was making his first league start of the season after signing from Wigan on Friday.
Both teams had contrasting results against Premier League opposition in the Capital One Cup in midweek, with the home side knocking out West Brom and reaching the quarter-finals for the first time in their history.
And things got worse for the Seagulls, who were knocked out by Tottenham, when captain Gordon Greer headed a fizzing Simon Francis cross into his own net to gift a 24th-minute opener.
If Bournemouth did not deserve their goal, Brighton definitely did when it came three minutes later through Adrian Colunga’s first of the campaign.
The Spaniard picked up on a defence-splitting pass from Joao Teixeira to round Artur Boruc and score only a second goal from one of the club’s strikers this season.
But the lead did not last long as Marc Pugh, fresh from his hat-trick last Saturday, saw his acrobatic volley fly past Al-Habsi via a deflection off the unlucky Dunk.
After the break Hyypia’s men continued to create opportunities to force the leveller and Dunk was inches away from heading a Jake Forster-Caskey free-kick past Boruc.
Steve Cook, playing against his former club, then had to make a diving interception to block Teixeira’s shot after a swooping break sent him through on goal.
When Baldock’s tidy finish from a ball forward from Al-Habsi made it 2-2 on the hour, Howe responded by hauling off the ineffective Brett Pitman and Matt Ritchie for Ryan Fraser and Kermorgant.
And despite not showing the form which has seen them talked about as potential automatic promotion candidates, they pushed forward in search of the three points.
Craig Mackail-Smith came on to try and rescue a draw but brave defending from Tommy Elphick denied him late on.