With Saturday's win, Doja Cat becomes the first female rapper and woman of colour to take top honours in the countdown.
The wildly popular song, from the artist's fourth studio album Scarlet, has topped music charts in more than a dozen countries including Australia.
Triple J music director Nick Findlay said he had little doubt Paint The Town Red would appear in the countdown when he first heard it in August.
"Over an iconic sample of Dionne Warwick's Walk On By, Paint The Town Red shows Doja Cat in her truest form: effortlessly shaking off the haters while flexing her uncanny ability at executing pure pop perfection," he said.
More than 2.3 million votes were cast for the 31st iteration of the annual youth music countdown which polled people on their favourite songs of 2023.
G Flip has smashed the record for the most entries in a single Hottest 100 with seven songs. (Joel Carrett/AAP PHOTOS)
Rounding out the Hottest 100 top three were Australians G Flip with their song The Worst Person Alive, and Dom Dolla with his song Saving Up.
With their second-place finish, rising indie pop-rock star G Flip smashed the record for the most entries in a single Hottest 100, with seven songs among the 52 Australian singles featured in the countdown.
The Melbourne-born artist ended the night with songs at number two, 22, 24, 26, 50, 65 and 80.
The previous record was held by Spacey Jane and Wolfmother, with six songs apiece.
Celebrating with their band crew and managers in the UK at 8am London time, the artist became emotional, thanking voters who supported them.
"I never thought I'd get so high," they said.
"I just put out music that I personally liked and I hope others did as well.
"I'm just so blessed and I'm just so grateful and everyone's made my life so amazing and it's just been so fun.
"Thank you to everyone who's come to the show or bought my record or voted for me."
Troye Sivan was one of 35 artists to make their Hottest 100 debut in Saturday's countdown. (Dan Himbrechts/AAP PHOTOS)
Electronic house music producer Dom Dolla also enjoyed a successful Hottest 100, securing two top-five entries as well as 18th place for his song Eat Your Man.
Pop superstar Troye Sivan is feeling the rush with a debut in the countdown alongside 35 other first-timers.
The Australian artist had three appearances, with his international hit Rush at number eight.
Pop princess Kylie Minogue made a long-awaited return, breaking the record for the longest time between Hottest 100 appearances with her hit song Padam Padam at number 48.
It was 26 years ago that she last appeared in the countdown with her song Did It Again in 1997.
Hip-hop group Hilltop Hoods extended their record for the most entries across countdowns with 24 songs.
The 100 songs that missed a spot in Saturday's countdown will get a spin in Triple J's Top 200 on Sunday.
HOTTEST 100 TOP FIVE SONGS
1. Paint The Town Red by Doja Cat
2. The Worst Person Alive by G Flip
3. Saving Up by Dom Dolla
4. Rhyme Dust by MK & Dom Dolla
5. Prada by casso x RAYE x D-Block Europe
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