The double Olympic champion fell ill earlier in the weekend and only made a late decision to take part in Clermont-Ferrand, where he cleared 6.06 metres at the first attempt to take victory.
Duplantis won his 37th consecutive meet, dating back to the summer of 2023.
Australia's Kurtis Marschall finished second (6.00m) with Greece's Emmanouil Karalis in third (5.90m).
"I'm OK. I'm scared of how I'm going to feel when the adrenaline runs off though. I'm super light. That's a good thing. You know, gravity doesn't like weight, so that's an advantage," Duplantis joked.
"I feel actually pretty decent all things considered."
Duplantis had three tries at breaking his latest world record set at last year's world championships, but he fell short of the bar at 6.31m in his first appearance since Tokyo.
"I feel like I'm in really good shape. I felt like I definitely could have jumped really, really high if it wasn't for the night before last, throwing up the whole night," said the Swede.
"But other than that I'm not gonna complain. I'm alive. And it feels like it's away now from the system."
Duplantis is planning to compete once more before the world indoor championships in Torun, Poland, next month. He will headline his home meeting, the Mondo Classic, in Uppsala on March 12.