Stoke's start to the 2019/20 campaign has seen just two wins in 14 Championship games, with only goal difference keeping them off bottom.
Since taking the job in January, Jones managed to record six victories in 38 attempts - posting a 16% win ratio.
In a statement, Jones said: "I would like to thank John and Peter Coates, firstly for the opportunity to manage this Football Club and then for the continued support and patience throughout my time here.
"I would also like to thank the supporters for their fantastic support. Finally, I wish the Club the very best for the future."
The Potters say that 'a new managerial appointment will be made as swiftly as possible' as they look to maintain their second division status.
Rory Delap, Kevin Russell and Andy Quy will take charge of first-team affairs in the interim period.
Stoke's next fixture sees them welcome West Brom in the televised game on Monday night.
