Wimmer, 24, sealed his move and signed a five-year contract with Mark Hughes' side on Tuesday, having completed his medical on Monday.
He becomes Stoke's seventh signing of the transfer window and the fourth defender to come in after the arrivals of Bruno Martins Indi, Kurt Zouma and Josh Tymon.
Stoke boss Hughes told his club's official website: "Kevin is an undoubted talent and he will significantly add to the quality of the group of players that I already have at my disposal.
"We put a real emphasis on trying to enhance the defensive areas of the squad this summer and we feel that we have been able to do that.
"We brought Kurt Zouma in earlier in the window and managed to bring Bruno Martins Indi back to the club following his loan spell last season, so bringing Kevin here too, a player I admire greatly, gives me real strength in depth in those central positions."
Hughes added: "Obviously this deal was with a view to the future because we know that Kurt is a Chelsea player, but Kevin is our player now and we knew that this deal wouldn't have been available to us this time next year.
"There is a lot of money being spent this summer, so for us to get a player of Kevin’s calibre through the door for the price we have paid, in my opinion, is something we will really appreciate for years to come."
Wimmer joined Spurs from Cologne for £4.3m in 2015, but only started 13 Premier League games over his two at the club and did not feature in any of their three league matches to date in 2017-18.
Tottenham's club-record signing of defender Davinson Sanchez from Ajax last week pushed him further down the pecking order.
The Austria international will compete for a starting spot with Martins Indi, on-loan Zouma, captain Ryan Shawcross and the versatile Geoff Cameron at bet365 Stadium.
Stoke, like Spurs, have four points from their first three Premier League games.