Morgan, who recently returned to action following an ankle ligament injury suffered during England's opening RBS 6 Nations game against Scotland this season, struck midway through the second-half.
It followed two first-half touchdowns from wing Jonny May, while fly-half Freddie Burns kicked 13 points. Saracens, meanwhile, remain top of the Premiership, their losing bonus point keeping them four clear after centre Joel Tomkins scored two tries, while Owen Farrell converted both scores and landed three penalties.
Gloucester made all the early running, going ahead through a fourth-minute Burns penalty before they carved out an impressive try scored by May, who cut inside Saracens full-back Alex Goode's weak challenge.
Farrell opened Saracens' account with a 35-metre penalty, and that was the cue for them to awake from their slumber as 10 points in five minutes saw them cruise ahead.
Tomkins finished superbly for a 21st-minute try, gathering the ball one-handed and throwing Gloucester's defence an exquisite dummy before touching down. Farrell converted and then added a penalty, underlining Saracens' ability to keep the scoreboard moving, but Gloucester were in no mood to take a back seat and they hit back spectacularly.
May swooped for his second try, touching down after he collected Burns' kick into space, and the fly-half converted before kicking a penalty that gave Gloucester an 18-13 interval advantage.
Farrell cut the deficit to two points with an angled penalty midway through the second period, setting up an intriguing final quarter that Gloucester launched in scintillating fashion. Morgan grabbed lock Lua Lokotui's pass from a restart, and then showed speed by shredding Saracens' defence through an angled run that saw him touch down at the posts.
Burns converted but the visitors immediately enjoyed a temporary one-man advantage when Gloucester scrum-half Dan Robson was sin-binned by referee J P Doyle for a professional foul. Saracens then cut the gap with Robson still off the field - Tomkins claiming his second touchdown and Farrell converting, making it 25-23 with nine minutes left.
It was a typically resilient effort by the visitors, who pushed hard for a winning score as the clock ticked down, but Gloucester did just enough to stay ahead and sign off at Kingsholm this term with a deserved triumph that was sealed by Burns' injury-time penalty.