His departure, by mutual consent, was widely anticipated following his talks earlier in the day with Stoke chairman Peter Coates.
"Stoke City and Tony Pulis confirm that they have mutually agreed that Tony will leave the club with immediate effect," the Potters confirmed in a statement.
Pulis, who following the retirement of Alex Ferguson and David Moyes' move into the Manchester United hotseat was the second-longest serving manager in the country, leaves Stoke in a far better position than he found them.
The 55-year-old was appointed Stoke boss for a second spell in 2006, and under his watch the club gained promotion to the Premier League in 2008 after a 23 year absence.
He led Stoke to their first FA Cup final, losing to Manchester City by a single goal in 2011, and as a result their first Europa League campaign.
The Welshman moves on 48 hours after the end of the 2012/13 season with Stoke finishing in 13th place.Contenders to succeed him in the Stoke dugout are Roberto Di Matteo, Gus Poyet, and early bookmakers favourite Rafael Benitez, the outgoing Chelsea interim manager.
The news was greeted with surprise by Stoke winger Matt Etherington who said: "I've spoken to a few of the other boys and they're shocked as well, it's hit us," he said.
"Fans were grumbling saying they wanted him out or wanted a change but it looks like they have got their wish.
"You have to be careful what you wish for in football sometimes. You look at Charlton under Alan Curbishley and look where they are now.
"Hopefully it won't go that way for us, hopefully we'll get someone in who will push us on and make us into a top-10 team.
"If you look at where Stoke were when he first came in - mid-table in the Championship - you can't argue he's done a fantastic job."