The 24-year-old, ranked 77th in the world, fell flat on his back in delight after claiming victory on the indoor hard court when Benneteau missed with a backhand down the line on his second matchpoint.
Sousa beat top seed and world number four David Ferrer in the last eight and then fourth seed Juergen Melzer of Austria in the semi-finals to reach his first final at the $875,500-event in Kuala Lumpur.
Dressed in black with his cap back to front, the young Portuguese right-hander struggled with his serve in the opening set as the experienced Benneteau broke twice to wrap it up 6-2.
The duo were on serve in the second before Sousa was forced to save a matchpoint at 5-4 down before holding and then snatching the crucial break to take the set 7-5 and force a decider.
The young Portuguese broke again in Benneteau's opening service game of the third set and he held firm, saving four break points to close out the set 6-4 and claim the breakthrough win.
The loss was tough on fifth seed Benneteau who was searching for his first ATP Tour title in his ninth final.