Wilshere looked a shoo-in for a place on the plane to Russia after making 38 appearances in all competitions for Arsenal this season.
But Express Sport discovered on Tuesday that Southgate had decided to omit Wilshere from his 23-man travelling party.
Southgate confirmed the news on Wednesday when he named his England World Cup squad, which included just five midfielders.
The England boss has now lifted the lid on why he opted against picking Wilshere, despite evidence he had put his injury woes behind him.
“Jack had good spell in the lead up to Christmas and just after, not as effective towards the end of the season,” said Southgate. “We think other guys deserve their place in the squad.”
Dele Alli, Eric Dier, Jordan Henderson, Jesse Lingard and Ruben Loftus-Cheek will be vying for a place in England’s midfield this summer.
The Three Lions warm up for the World Cup by taking on Nigeria at Wembley and Costa Rica at Elland Road at the start of June.
They kick off their tournament in Russia by taking on north African opponents Tunisia in Volgograd on June 18.
England follow up their showdown with Tunisia by facing central American minnows Panama in Nizhny Novgorod six days later.
And Gareth Southgate’s men conclude their Group G fixtures by going head-to-head with Belgium in Kaliningrad on June 28.
Wilshere, who last played for England at Euro 2016, was joined in being left at home by fellow seasoned pro Joe Hart.
Wilshere responded to Southgate’s by publically making plans for when the World Cup is on on social media.