Maertens touched the wall in a time of 3:41.78 to finish 0.43 seconds ahead of Australian silver medallist Elijah Winnington and South Korean bronze-winner Kim Woo-min at La Defense Arena.
Maertens from Magdeburg, came into the race with the fastest time this year and duly converted on the biggest stage to become the first German winner in the event since Uwe Dassler took the title for East Germany at the 1988 Seoul Games.
His victory erases his record as a nearly-man in men's swimming, following two bronzes and a silver at the last three world championships.
He made a barnstorming start, shooting out to a big lead ahead of a trio of world champions in Kim, Winnington and Australia's Sam Short.
The German raced at world record pace until the final 50 metres, and that proved enough despite a fast finish by Winnington, who claimed his second Olympic medal.