The Saddlers are 14th in the table, six points above the relegation zone.
Whitney had been at the Banks’s Stadium for 15 years, joining the club as a physio in 2003.
A club statement read: ‘We thank Jon for his hard work, effort and service during his time at the club but feel that a change in management is in the best interests of the football club at this stage.
‘The club will now go through the necessary recruitment process.’
Ian Sharps has been placed in temporary charge of first-team affairs and will be assisted by John Ward.
England manager Gareth Southgate has claimed that the country needs to boot racism out of its own football before criticising World Cup hosts Russia.
Newcastle have been linked with a shock move for former Sunderland goalkeeper Simon Mignolet during the summer.