The 2017 world champion scored 8552 points, well down on his world record of 9126 but easily in excess of the Olympic qualifying standard of 8350.
This was the Frenchman's first decathlon since last year's Doha World Championships where he was eventually forced to withdraw having pulled his hamstring during the 110m hurdles.
That turned out to be his best event on the Indian Ocean island, Mayer clocking a personal best 13.54s at the start of day two.
The 28-year-old sported a new streamlined look for the closing 1500m, having his head shaved after the javelin.
Mayer crossed the line in, by his standards, a pedestrian 4:47.74 to win the event with Taavi Tsernjavski second on 8030 points.
Another Estonian, Risto Lillemets, was third with 7993 ahead of Axel Hubert of France on 7980.
Mayer held a comfortable lead overnight with a day one total of 4350 points.
After clocking a solid 10.68s to win the 100m, he went out to 7.40m in the long jump, 40 centimetres down on his personal best.
He claimed his second event victory with 16.20m in the shot before clearing 1.97m in the high jump.
In the final event of the day he ran the 400m in 48.87s, just over six-tenths outside his lifetime best, but showing his flat speed is right where it needs to be.
He confirmed that in the first event of day two, eclipsing his previous 110m hurdles personal best by one-hundredth of a second.
Then came a decent 50.32m in the discus followed by his worst event of the competition, the pole vault where he only managed 4.65m having cleared 5.45m in the past.
A 70-metre javelin thrower on his day, Mayer sent the spear out to 67.66m as he closed in on his target.
He only needed to get round in the 1500m to break the Olympic qualifying standard, and he jogged home in a time almost 30 seconds down on his best to book his ticket to Tokyo.
Colombian record holder Evelis Aguilar won the heptathlon with a score of 6055 points, well down on the women's qualifying standard of 6420.
Estonia's Mari Klaup was second with 6014, just four points ahead of Austria's former world U20 champion Sara Lagger.
Hanna Kasyanova of Ukraine, who was world champion in 2013, was fourth on 5782.