Murray took to social media to slam Martin Solveig after he asked Norwegian footballer Ada Hegerberg if she knew how to perform the raunchy dance move - an example of "the ridiculous sexism that still exists in sport".
A clip from the ceremony of the DJ asking the 23-year-old Norwegian if she could twerk and her responding "Non" in French quickly racked up millions of views.
"I'd like to say a big huge thank you to France Football for letting us have this opportunity to have this award".
Hegerberg then said she was "just happy" to have won the Ballon d'Or "to be honest".
"I, of course did not want to offend anyone", Solveig said.
The last player to lift the award apart from the Argentine and Portuguese, who have won it a joint-record five times each, was Kaka in 2007 when the Brazilian played for AC Milan.
Lyon also won the French title for the 12th season in succession, with Hegerberg top-scoring with 31 goals, and she continues to bang in the goals for her team who are top of the table again this season.
After Hegerberg took the stage and raised her trophy triumphantly, Solveig interviewed her briefly.
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It seemed as though United would go on to win the game but their display in the second half was flat and uninspiring. Manchester United goalkeeper David De Gea has turned down a deal worth £275,000 a week to stay at the club.
"It is a huge step for women's football and the work you have put down is such an important thing for women's football and together we will make a difference". When Hegerberg renewed her contract with Lyon until 2021, it was widely rumoured she'd become the highest paid player in the women's game, although her official salary details were not released. "It's all about how we respect women's football".
Hegerberg is a three-time Women's Champions League victor with French side Lyon and scored a tournament-record 15 times last season.
The Norwegian victor made history by becoming the first to receive the honor of Ballon d'Or's inaugural title as the best female player in the world.
"What questions did they ask [best men's under-21 player Kylian] Mbappe and [best men's player Luka] Modric?" I didn't really consider it a sexual harassment or anything in the moment.
A jury of 45 journalists picked Hegerberg from among 15 nominees, including Matildas star striker Sam Kerr who was fifth in the voting.
The prolific striker has abstained from playing for Norway's national team since 2017 because of the country's treatment of its women's national team.
"It's not that often that I use the word "proud" but today I'm really proud", she said.
But she also expressed frustration with the uneven pace of progress for women.