Stokes suffered a cartilage tear in his left knee during England's crushing Test victory against Sri Lanka last week at Headingley.
He had already said that he expects to miss the remainder of Sri Lanka's tour, but the England and Wales Cricket Board have not offered any prognosis following his operation yesterday.
Stokes is unlikely to be seen again until the start of the Pakistan series in July, though England are not yet committing to a timescale.
The 24-year-old admitted it was a huge blow to be sidelined while England are in action, although he planned to watch his team-mates in the second Test against Sri Lanka in Durham this week.
"Devastated to be missing the rest of the series, this has been a ongoing issue for 2/3 years which I've managed to play through until now," Stokes tweeted.
"All the best to the lads in the rest of the series, see you down at Durham in the crowd."
Devastated to be missing the rest of the series,this has been a ongoing issue for 2/3 years which I've managed to play through until now...
Devastated to be missing the rest of the series,this has been a ongoing issue for 2/3 years which I've managed to play through until now...— Ben Stokes (@benstokes38) May 23, 2016
In Stokes' absence, Warwickshire's Chris Woakes, who took nine wickets on Monday to celebrate his call-up for the second Test against Sri Lanka, and the uncapped Jake Ball will have the chance to impress.
"Ben Stokes has undergone surgery this afternoon to address a cartilage tear in his left knee. Full details on the length of his rehabilitation will be confirmed in due course," an ECB statement read.
Topley's situation is clearer, with "a partial stress fracture of the lumbar spine" likely to keep him sidelined for most of the season.
Hampshire seamer Topley, who was in England's World Twenty20 squad, has been out since April 16 with a fractured thumb but now has much bigger problems to contend with.
"Reece Topley has been diagnosed with a partial stress fracture of the lumbar spine and will require a significant period of rehabilitation," the statement added.
"He will miss the next three months and will aim for a return for Hampshire before the end of the season."
There was better news for David Willey, who has a small abdominal tear and is aiming to make his return to action in Yorkshire's Twenty20 Blast match at Worcestershire on June 2.