All-rounder Moeen Ali will return home despite taking eight wickets in the second-Test defeat by India, his first Test since 2019.
He returned match figures of 8-226 in the 317-run defeat in the second Test in Chennai, his first Test since August 2019.
The 33-year-old contracted coronavirus on the tour of Sri Lanka in January and spent 14 days in isolation.
“Moeen has chosen to go home. It’s come to a point where he wants to get out of the bubble,” said captain Joe Root.
“This tour has been really difficult for him, dealing with Covid and being in his room for such a long period of time.
“We said at the start if players feel like they need to get out of the bubble that would be an option, and it’s important we stand by that.”
Moeen departure ‘absolutely staggering’
England have implemented a rotation policy to help manage players’ workload in a busy year that includes a possible 17 Tests and a Twenty20 World Cup.
They are also mindful of the wellbeing of the players with so much time spent in bio-secure ‘bubbles’ since the outbreak of coronavirus.
Former England captain Michael Vaughan described Moeen’s departure as “absolutely staggering”.
He told the Test Match Special podcast: “You’ve just got back into the Test team, get all these wickets, smashed a few into the stands and now England are sending him home.”
Moeen was recalled for the second Test at the expense of off-spinner Dom Bess, one of four changes to the side that won by 227 runs in Chennai last week.
England’s all-time leading wicket-taker James Anderson was rested, wicketkeeper Jos Buttler returned home after the first Test and pace bowler Jofra Archer missed out with an elbow injury.
“I just don’t understand this scientific approach to selection, how they’re not being flexible to keep players there who have suddenly done something,” said Vaughan.
“I just don’t quite understand why a series like India away, which is such a huge series in the Test calendar, you’d be swapping and changing your side so much.”
Archer and Ben Stokes sat out both Tests in Sri Lanka, while Jonny Bairstow, Sam Curran and Mark Wood missed the first two Tests in India.
‘He wants to be at home with his family’
Moeen took a break from Test cricket in 2019 and struggled to regain his place before being recalled for the 2-0 series win in Sri Lanka.
He took 4-128 and 4-98 in the second Test against India, and his tally of 49 runs – including 43 off 18 balls as England’s defeat was confirmed on the fourth afternoon – was more than any other England player.
“It wasn’t about us asking Moeen if he wanted to stay. It was a decision that he chose,” said Root.
“We want as many of the players to be available for as long as possible, but we also want them to be comfortable here.
“He feel he wants to be at home with his family and we completely respect that.”
While England have rotated players for Tests, their squad for the five-match Twenty20 series in India that starts on 12 March is full strength as Eoin Morgan’s side prepare for the T20 World Cup in India in October.
Moeen is in that squad and will also be part of this week’s auction for the Indian Premier League, which runs from April to June.
Vaughan, who captained England in 51 of his 82 Tests, said: “This year is about winning the Ashes. I know there’s a T20 World Cup but for English cricket it’s about getting those Ashes back.
“Surely the Test team takes preference over the T20 team. They should be getting all their eggs into the basket to make sure by the time they get to Australia they’re a team that has played a lot of cricket together.”
The third Test of England’s four-match series in India starts on 24 February in Ahmedabad.
BBC cricket correspondent Jonathan Agnew
Moeen has not had a great time. But he got himself back in the side and scored some runs, hit the ball sweetly at the end, and took some wickets. Now he is going home.
Joe Root and the management made it clear at the start of the tour that if a player wanted to go home, he will go home. That has always been a part of the deal. So they cannot turn round to Moeen and say ‘you are not going home’.
It is just a really difficult situation. Moeen had 10 days or so stuck in a room in Sri Lanka after testing positive so he clearly has not had an easy time. It will have been a difficult decision for him.