The Everton defender has been consistently linked with a move to the Etihad Stadium this summer and is now expected to join Pep Guardiola's side imminently.
City were required to submit a squad list of up to 25 players on Monday ahead of a two-legged qualifying tie against Steaua Bucharest.
According to Uefa, Stones was included in the list received from City prior to Monday's midnight deadline.
"Uefa received all Uefa Champions League playoff squad lists ahead of the midnight CET deadline on Aug. 8," European football's governing body said in a statement.
"As is standard procedure, the lists were automatically published on Uefa.com once they were approved and entered into the Uefa competition database."
Stones, who appears to have been handed the no 24 shirt at City, is still named as an Everton player on the Merseyside club's website.
A City source reportedly told Sky Sports News that the leak of Stones' transfer was a "huge embarrassment".
Eliaquim Mangala, whose place in central defence would be threatened by Stones' arrival, is not listed in the 21-man sqaud.
Wilfried Bony and Samir Nasri are also omitted, with the club willing to listen to offers for all three players.
The injured pair of Vincent Kompany and Ilkay Gundogan are absent on account of their fitness.
City travel to Bucharest on 16 August, with the return leg played on 24 August.
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