Metz substitute Yann Jouffre provided the decisive moment of a dull contest eight minutes from time when goalkeeper Yohann Pele failed to deal with his 20-yard free-kick.
Payet left West Ham United in a £25 million ($40.62 million) move last weekend and made his second Marseille debut as a substitute in a Coupe de France victory over Lyon in midweek.
The France international was again left on the bench until the 55th minute, when he joined the action along with Marseille's top scorer Bafetimbi Gomis.
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Within two minutes, Gomis had the ball in the Metz net after Payet's free-kick had been flicked on, but the on-loan Swansea City striker was correctly ruled offside.
Simon Falette then diverted Payet's teasing ball onto his own crossbar before Jouffre's finish five minutes later took Metz four points clear of the relegation zone.
