The midfielder’s header ended up shading a low-key encounter at The Valley against a Charlton side that lacked a cutting edge.
Hughton, sacked by Norwich at the tail end of last season, was hired to replace Sami Hyypia following the former Liverpool defender’s pre-Christmas resignation.
He tasted victory at the first attempt as Albion won 2-0 at Brentford in the FA Cup last week and has now seen his side move further away from the relegation places.
Brighton almost took an early lead when Charlton goalkeeper Neil Etheridge dropped a high ball but Solly March’s shot was blocked by a defender.
George Tucudean’s first-time effort suffered a similar fate at the other end, with Lawrie Wilson firing the rebound over the bar.
Etheridge was behind Sam Baldock’s header before getting to a long ball ahead of the onrushing March.
Brighton were the better side and caused Charlton problems with their quick passing, although when Joe Bennett was brought down on the edge of the box Danny Holla wasted the opportunity with a poor free-kick.
Charlton were sluggish but almost made the breakthrough on the half-hour mark when Andre Bikey forced Albion goalkeeper David Stockdale into a save from a position in a crowded goal-mouth.
Igor Vetokele headed wide as the home side roused themselves again and Wilson was unfortunate to see the ball go over after he stuck out a leg for an instinctive flick.
Stockdale then had to dive at Tucudean’s feet after Vetokele tried to put his strike partner through and captain Johnnie Jackson saw an effort saved by Stockdale, before Bennett survived a strong appeal for handball in the Brighton box just before the break.
Charlton had Etheridge to thank early in the second period for denying Jake Forster-Caskey after the midfielder was put in beyond the home defence.
Tony Watt replaced Tucudean and the former Celtic striker soon forced Stockdale into a near post save from a tight angle following a run into the box.
Both sides were looking more likely to score now, with Bennett’s back-post header saved by Etheridge and Chris Solly thumping the Brighton bar from 25 yards out.
The goal arrived in the 62nd minute, with Ince rising at the back post to head home a free-kick delivery by March.
Stockdale preserved the lead by keeping out Vetokele’s header and Watt fired another good chance wide on the volley.
Charlton threw men forward in the closing stages but could not force an equaliser.