Yaqeen Ahmed contributed 11 points in a disciplined South African performance at the Mikheil Meskhi Stadium, where a dominant set-piece, flawless goal-kicking and resolute defence secured the win.
The victory also made Kevin Foote's side the first South African U20 team to win back-to-back Junior World Championship titles.
The final in Tbilisi was delayed by 45 minutes due to inclement weather, and both teams were forced to adapt to the wet conditions over the course of the contest.
Ahmed slotted a penalty goal in the eighth minute to earn his side some reward for their set-piece dominance, but France continued to press throughout the first half.
Ahmed added a second penalty on the stroke of half-time to extend the lead, but it was France who seized the initiative at the start of the second stanza, thanks to a try by flanker Raphael Audebert.
The French may have added a second if not for a timely intervention by the South African defenders on their own line, and from there, the Junior Boks managed to exit their half.
Replacement centre Samuel Badenhorst was denied a try in the 57th minute after the TMO called play back for a foot in touch during the buildup.
Eventually, the dam wall broke, with centre Markus Muller scoring in the 67th minute, and Ahmed adding the extras to give the Junior Boks an eight-point lead.
The Junior Boks had two further tries chalked off in the closing stages â- by Cheswill Jooste and Ahmed â- but they continued to press the French defence, and were awarded a penalty in the final moments.
From there, Ahmed stepped up to slot the goal and secure a 16-5 win.
The result caps a successful Junior World Championship campaign and season for the Junior Boks, who also won the U20 Rugby Championship earlier this season.
What's more, it extends the Junior Boks' unbeaten run to 18 matches, a run that began at the 2025 Junior World Championship in Italy.