Etzebeth, captaining the side after the late withdrawal of number eight Warren Whiteley, completed an excellent set-piece move to go with scores from centre Jesse Kriel, hooker Malcolm Marx and scrumhalf Rudy Paige.
All France’s points came via the boot of flyhalf Jules Plisson, who kicked four penalties as they struggled against the physicality of the home side in an error-strewn performance.
The victory was a first for the Boks over France in five tests at Ellis Park, and comes after they lost eight of their 12 internationals last year in what was the worst season in the country’s history.
"This was a huge step in the right direction for us," Bok coach Allister Coetzee told reporters.
"Test match rugby is always about winning, not about being pretty. We did not execute as well as we wanted to, but the courage of the team was great."
An early Elton Jantjies penalty put the home side in front, and their energetic start was rewarded with the opening try inside seven minutes.
Centre Jan Serfontein supplied the pressure from a long kick into the French 22 and when the Boks were able to complete the turnover, Kriel slid in at the corner.
The teams traded penalties as the Boks went into the break with a 16-9 advantage in front of the best crowd of the series, 55,820.
They turned down three easy points after winning a penalty early in the second period and opted for a set-piece in the corner for what turned out to be an excellent training-ground move that bamboozled the visitors.
Serfontein rose in the middle of the lineout and fed massive lock Etzebeth, who got a running start five metres from the line and crashed over for the try.
Both sides committed errors in attack, which affected the flow of the game, but just past the hour mark the Boks crossed for their third try.
A break from replacement lock Pieter-Steph du Toit took the home side into the French 22 and powerful hooker Marx scored under the posts before Paige grabbed a first test try with five minutes remaining.
(Reporting By Nick Said,; Editing by Neville Dalton)
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