Josh Hathaway and Jack Clement scored Gloucester's tries, both of which Santiago Carreras converted, in the first half against a Quins side featuring several England internationals including Marcus Smith.
The result left Gloucester fifth in the table and level on points with fourth-placed Saracens, while Harlequins stay seventh with 19 points from seven games.
Harlequins' defeat meant they finished with zero points in a league game for the first time since losing 39-0 against London rivals Saracens in September 2014.
Gloucester coach George Skivington said: "Our defence was outstanding as to 'nil' any Premiership side is massive, especially one as good as Quins.
"The boys are now finding the right balance between attack and defence but our defensive set in the first 10 minutes set the tone for the rest of the match.
"Quins wanted to play attacking rugby just like us but we got on top of them today, although we left four or five tries out there."
Harlequins counterpart Danny Wilson said: "We were riddled with errors and physically we weren't at the races, especially in the first half as Gloucester clearly had the competitive edge at that stage.
"The second half was an improvement but overall we gave away 23 turnovers and made 15 handling errors - but despite that we still had many opportunities to score, which we blew."
Before kick-off, both sides paid tribute to former Gloucester wing Tom Voyce, who died during the floods of Storm Darragh earlier this month.