The Cardiff match failed to hit the heights as a spectacle, with poor kicking and numerous errors contributing to a scoreless second half.
After Leigh Halfpenny opened the scoring with a penalty, the fullback, a nominee for the International Rugby Board's player of the year award, helped set up the first try after 15 minutes.
Halfpenny made a short break before slipping the ball to centre Owen Williams who shrugged off two weak tackles on his way to the line.
Nine minutes later the Welsh backline were in action again, Ashley Beck showing some deft footwork by the left touch line before reaching out to score following a barnstorming run from George North.
Handling errors and a misfiring lineout prevented Tonga stringing together a meaningful period of possession until they rallied with a try before the break, an offload from Viliami Ma'afu helping set up wing Viliami Helu and his angled run beat the home defence.
Gatland made 11 changes from the Argentina win, helping to explain a somewhat disjointed effort by the home side.
One of the newcomers - 19-year-old Hallam Amos - went close to scoring on his debut early in the second half when he had his foot dragged into touch by Siale Piutau's covering tackle.
Luke Charteris had the ball dislodged while attempting to force the ball down after 62 minutes while North had a try disallowed for obstruction as Wales failed to breach the Tongan defence for more than 50 minutes.
Wales host Australia in the final match of their November series next week.
(Reporting by Josh Reich; editing by Tony Jimenez)
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