England have already confirmed their key all-rounder will miss the second Test of three, starting at his home ground in Chester-le-Street on Friday, after scans on the left knee he jarred during the innings victory at Leeds.
The 24-year-old has been replaced in a 12-man squad for the Durham Test by fellow all-rounder Chris Woakes.
Depending on the outcome of a consultation with a specialist on Tuesday, it is understood he may be out for four to six weeks.
Surgery is one option if a cartilage problem is confirmed - and with the five-match Royal London Series beginning on June 21, and one-off NatWest T20 international on July 5, England will probably be disinclined to take chances with such an important player before four Tests against Pakistan, beginning on July 14 at Lord's.
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Woakes and Jake Ball - the seamer who was picked in a Test squad for the first time at Headingley - will join England's squad in Durham, after leaving their ongoing matches in the Specsavers County Championship on Monday evening.
Stokes, meanwhile, is set to discover how long he is likely to be absent.
An England and Wales Cricket Board statement on Monday morning read: "England all-rounder Ben Stokes will miss the second Investec Test at Emirates Riverside after sustaining a left knee injury during England's first Test victory at Headingley.
"Following a scan (on Sunday) and review by the medical team, it was advised that Stokes would be unavailable for the match in Durham.
"The 24-year-old will be reviewed by a consultant (on Tuesday), to decide on a management plan."
Woakes is back in the reckoning for his seventh cap - his last came at Centurion in January, when England lost the match but won the series against South Africa.
The Warwickshire all-rounder will vie with Nottinghamshire seamer Ball for the final place to face Sri Lanka, depending on the balance of the team England decide is needed.
They may also face a new opponent at Chester-le-Street, after Sri Lanka chief selector Sanath Jayasuriya confirmed wicketkeeper-batsman Kusal Perera is to join the tourists' squad.
Perera was cleared to play again two weeks ago, after the International Cricket Council withdrew a provisional doping ban and all charges against him.
His arrival, possibly in time for the second Test, will alter the balance of Sri Lanka's squad - because he will replace injured seamer Dhammika Prasad.
Jayasuriya told Cricinfo: "Kusal will join the team as soon as possible and acclimatise, so he can do some serious work with the bat."