Newcastle announced the news on Wednesday and confirmed assistant manager Jones, who was also number two to Roberto Martinez at Goodison Park, will lead the team on an interim basis.
Starting with this weekend’s clash with Crystal Palace, he will be supported by the coaching team of Steve Agnew, Stephen Clemence, Ben Dawson and Simon Smith.
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The 51-year-old, who was born in Gateshead, joined Newcastle in January 2021 after leaving his role as first-team coach with Bournemouth and was also part of Gareth Southgate’s England staff for Euro 2020.
A former forward with Wigan, Jones followed Martinez to Everton in July 2013 and left Merseyside when the Spaniard was dismissed by the Toffees in May 2016.
Jones also worked alongside Martinez with the Belgium national team.
Steven Gerrard and Wayne Rooney are names who have been tentatively linked with taking on the Newcastle job full time.
Speaking last week, Liverpool legend Gerrard, who has been tipped to one day take over from Jurgen Klopp at Anfield, said: “I think it’s interesting, what’s happening at Newcastle.
“I think if anyone deserves a break it’s the Geordie fans. So I’m sure that excitement levels are very high down on the Toon.
“And obviously everyone connected with the game is looking in with interest, to see how that develops.
“But from a personal point of view, I don’t really get involved in speculation. And I wish Steve Bruce all the best.”
Former Everton star Rooney, meanwhile, insists he is focused on his current job as manager of Derby County in the Championship.
“I saw that this morning [Tuesday],” Rooney told DerbyshireLive of reports linking him with the Magpies.
“From my point of view I cannot stop speculation, I get that, but I have had no contact at all with Newcastle United and obviously, as I have stated before, I am committed to this football club.”
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Paulo Fonseca, Eddie Howe and Lucien Favre are currently the shortest odds with the bookies to replace Bruce.
After two years as Newcastle manager, Bruce said: “I am grateful to everyone connected with Newcastle United for the opportunity to manage this unique football club.
“I would like to thank my coaching team, the players and the support staff in particular for all their hard work. There have been highs and lows, but they have given everything even in difficult moments and should be proud of their efforts.
“This is a club with incredible support, and I hope the new owners can take it forward to where we all want it to be. I wish everyone the very best of luck for the rest of this season and beyond.”