Sousa, the world number 77 from Portugal, was forced to fend off match point when trailing the experienced Frenchman 2-6 4-5 before coming through for a hard-fought 2-6 7-5 6-4 victory in two hours and 18 minutes.
The 24-year-old saved six of eight break points to frustrate world number 33 Benneteau, who has now failed to win in nine ATP final appearances.
Sousa said on atpworldtour.com: "We both played a great match. He had a lot of chances to win."
Sousa's unexpected triumph makes him the seventh first-time winner on the ATP circuit this season - and the first-ever title winner from Portugal.
"I'm so tired mentally and physically but I just feel amazing," added Sousa, who defeated top seed David Ferrer en route to the final.
"It's just a dream come true, winning my first title here in Malaysia."
A downbeat Benneteau was frustrated at being unable to finally break his title duck.
"I tried everything today. I played very well, I was very aggressive and I didn't let him play for two sets," he said.
"At 5-4 I had match point and I played the point perfectly. He made the passing shot down the line with his forehand.
"I took my chance, it didn't pay off and it's hard, it's very hard. But it's sport.
"It's tough because I was leading the match, but this is tennis."