Lewin, attending his 205th match as England physio, suffered the injury when he jumped up to celebrate Daniel Sturridge's equaliser in Manaus and came down on a water bottle, twisting his ankle.
Scans revealed he had dislocated and fractured his ankle in what manager Roy Hodgson described as a "very painful" accident.
Lewin flew back to Rio from Manaus with the team but whilst the squad will head on to Sao Paulo later this week for Thursday’s crunch clash with Uruguay, the Arsenal man – England’s physio since 1996 - will be flying home to the UK.
Lewin said: "I'm absolutely devastated to be going home. A lot of hard work, planning and preparation have gone into this tournament.
"England has a fantastic backroom staff who will continue to provide excellent support to the players and management.
"I'd like to thank my England colleagues and the FIFA medical officers at the Amazonia Arena for their excellent, professional treatment.
"And of course, I wish the England team all the best for the rest of the tournament."
Hodgson said: “It's very unfortunate for Gary and us that this accident occurred. We will of course miss him as he's an extremely experienced and popular member of staff.
"However, we wish him a speedy recovery and know he'll be cheering us on from back home."
Lewin is the second England staff member to suffer an injury on this tour.
Assistant coach Ray Lewington needed surgery on his knee after waking up in agony during the squad's warm-up camp in Miami.
Lewington has remained with the squad, although he has been given a cast for his left leg.