The 27-year-old joined City from Swansea City for a reported fee of £25 million in January 2015, but has made only 46 appearances since then, scoring 10 goals.
Stoke announced the signing on their official Twitter page.
BREAKING | #SCFC delighted to announce the season-long loan signing of @wilfriedbony from @ManCity pic.twitter.com/0I0FO81UDd
— Stoke City FC (@stokecity) August 31, 2016
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Bony was pictured holding a club shirt at Stoke's training ground. He had earlier tweeted: "It's a new day and I look forward to a new exciting challenge."
Bony has made 44 appearances for the Ivory Coast, scoring 13 goals, and was a member of the team that tasted glory at the 2015 Africa Cup of Nations in Equatorial Guinea.
He was signed by City to provide back-up for Sergio Aguero, but young Nigerian striker Kelechi Iheanacho moved ahead of him in the pecking order.
Bony has not featured for City this season under new manager Pep Guardiola.
He follows Joe Hart in leaving the Etihad Stadium on loan on transfer deadline day. Hart earlier finalised a move to Italian side Torino.
"Everyone at City would like to wish Wilfried the best of luck," City wrote on their website.
Bony is Stoke manager Mark Hughes's fourth new recruit after Wales midfielder Joe Allen, Egyptian winger Ramadan Sobhi and Irish defender Ryan Sweeney.
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