The win keeps the Welsh region's hopes of progressing to the knock-out stages alive, although it leaves Gloucester, who were indebted to a converted try from centre Billy Burns, with only one win from three games.
With the Scarlets having 11 players away with the Wales squad and a handful of injuries they were forced to field a mixed side of youth and experience led by Josh Turnbull.
Gloucester, whose director of rugby is former Scarlets boss Nigel Davies, included former Parc y Scarlets favourite Tavis Knoyle.
Gloucester were also captained by Welshman Will James, who is set to retire at the end of the season and had to go off midway through the first half with concussion.
Before the kick-off there was a minute's silence in memory of Llanelli RFC legend Hefin Jenkins who died earlier on Friday.
He played more than 400 games for the club including the famous 9-3 victory over New Zealand in 1972.
Neither side were able to impose themselves in the opening quarter in the wet conditions.
The only hint of a score early on came with a hack through from wing Drew Cheshire but home wing Kristian Phillips was on hand on the line to secure possession.
The Scarlets' first visit to the opposition 22 ended with them conceding a penalty and when a real chance opened up for Phillips his pass to Turnbull in space ended up going forward.
The home side did well to battle their way in to Gloucester's 22, employing pick and go tactics, only to concede another penalty.
The stalemate was eventually broken after 34 minutes courtesy of a try for centre Hughes, the Wales Under-20s captain, who went in at the left corner.
It came via a cross kick from outside-half Josh Lewis which was picked up by full-back Jordan Williams, who put Hughes into the corner. Lewis failed to convert from the touchline.
That was the only score of a pretty uneventful first half with the Scarlets taking a 5-0 lead into the break.
The third quarter took on a familiar theme of being scoreless until Cherry and Whites' centre Burns burst through an attempted double tackle and slid in for the equalising try after 55 minutes. Burns converted to give Gloucester the lead.
The visitors' advantage only lasted five minutes as Lewis kicked a penalty goal inside Gloucester's 22 to give the Scarlets an 8-7 lead.
Gloucester had a golden opportunity to regain the lead but Burns was short of the mark with a 40-metre penalty shot.
It was a key moment and three minutes from time the Scarlets sealed the win with a try for wing Aaron Warren who ran in from 25 metres out.
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- Parc y Scarlets