It was his 15th and final victory of a year in which he improved his own world record three times, up to 6.26 metres.
The US-born Swede was again a world apart from the competition at the King Baudouin Stadium in cold conditions.
He vaulted only three times, at 5.62, 5.92 and 6.11m, the latter a new meeting record. Greece's Emmanouil Karalis was second with 5.82m on countback from home favourite Ben Broeders.
"My legs felt terrible tonight and I'm just really tired," admitted Duplantis, who was left ruing taking on hurdles star Karsten Warholm in a pre-event exhibition 100m race in Zurich last week.
"That took a lot more from my body that I expected. With 6.11 metre I got a good result, but the world record wasn't meant to be tonight."
Duplantis added: "Now it's time to celebrate my beautiful season: I will drink some good Belgian beers tonight for sure!"
The opening session of the two-day finals of track and field's elite ciruit was high-octane affair, with a large percentage of some of the 82 medal winners from the Paris Oympics on show.
Olympic champion Julien Alfred scorched to victory in the 100m as US rival Sha'Carri Richardson finished well down the field.
It had been Richardson who triumphed in Zurich last week, edging Alfred at the line.
But the Saint Lucia sprinter turned the tables when it mattered, clocking 10.88 seconds for the win. Richardson eased off well before the line in the knowledge she had been well beaten, eventually finishing eighth in the nine-woman field in 11.23sec.
"I am so happy, it feels amazing to finish my season on a good note and to take the win," said Alfred.
Well-played cameo
American star Sydney McLaughlin-Levrone played her cameo to a tee.
The 25-year-old, who improved her own world record when winning back-to-back Olympic 400m hurdles golds in Paris, had not competed at a Diamond League event this season and was therefore ineligible for the finals.
But organisers managed to lure McLaughlin-Levrone, who won a second Olympic gold in Paris with the US 4x400m relay team, to Belgium to race in invitational 200 and 400m flat races as a way to "honour" her Olympic achievements.
She won her 400m race in 49.11sec, which was better than world and Olympic champion Marileidy's winning time of 49.45sec in the 400m final proper.
Norway's Jakob Ingebrigtsen held off a strong field for victory in the ever-competitive men's 1500m in 3min 30.37sec.
The Tokyo Olympic champion missed out on the podium in the French capital, but has been keen to make amends, once again holding off Kenya's Timothy Cheruiyot and Paris Games winner Cole Hocker.
Ukraine's Yaroslava Mahuchikh, the world and Olympic champion and world record holder, notched up her eighth consecutive Diamond League win with a best of 1.97m, winning on countback from Australian Nicola Olyslagers.
But there was a rare defeat for Morocco's Soufiane El Bakkali, the double Olympic gold medallist and two-time world champion, in the men's 3000m steeplechase.
Kenya's Amos Serem claimed the win in 8:06.90, with the Moroccan coming in second in 8:08.60.
Jamaica's Ackeem Blake strode home in the men's 100m, winning in 9.93sec ahead of Americans Christian Coleman (10.00) and Fred Kerley (10.01), the Olympic bronze medallist and 2022 world champion.
Blake's teammate Tajay Gayle, the world bronze medallist, won the long jump with a season's best of 8.28m, Olympic champion Militadis Tentoglou coming in third, 1cm behind Switzerland's Simon Ehammer (8.16m).
And there was a surprise win for Britain's Charles Dobson in the men's 400m, laurels taken in 44.49sec.
American Valarie Allman won the women's discus with a best of 68.47m and echoed many athletes' sentiments after a long year of track and field.
"Now it's off season! I really can't wait for your fries, waffles and chocolate!"