The Repsol Honda rider suffered torn ligaments and fractures to his ankle, tibia and fibula in last weekend's practice accident but nevertheless went on to compete in the race, finishing an impressive fourth.
However, Sunday's race at the twisting Brno circuit has been deemed a step too far for the Australian, who trails Jorge Lorenzo by 39 points with seven rounds remaining.
Stoner, whose hopes of a third world title will be severely dented by his withdrawal from this weekend's race, will hold a press conference later today [Thursday].
"Casey Stoner will miss the bwin Czech Republic Grand Prix as he has to head back to Australia to undergo treatment on his ankle injury sustained last weekend in Indianapolis," read a statement on the official MotoGP website.
"Stoner will leave Brno this evening for Australia after his doctors advised him to have surgery on his damaged ankle."
Stoner, who is to retire at the end of this season, had previously voiced his fear that the round at Brno would represent a stern test of his fitness.
"I'm not feeling too optimistic for Brno after a tough weekend in Indy," he said earlier this week.
"In Brno there are many changes in direction and a lot of right hand corners so there will be a lot of weight on my ankle and it's going to be very difficult."
He told a press conference: "It's disappointing news but it's finished our championship.
"I've no idea when I'll be back as until we've had the surgery we won't know." He added: "The plan is to get back to Australia as we have to wait for the inflammation to go down before having surgery.
"We already have everything lined up to see what we can do and then try to get back.
"Normally my doctor doesn't have a problem with me riding with injury but as soon as he read the report he advised me against riding in Indianapolis.
"All the different reports have been the same, that I need to get off this foot as soon as I can.
"My plan is to come back hopefully a race or two before (the Australian Grand Prix at) Phillip Island but I don't know.
"To have these kind of disappointments is frustrating, especially in my last year. But that's racing.
"I'm not in this championship to finish on a fairytale. I'm not always going to keep waiting for a fairytale ending."
While Stoner sidelined his team-mate Dani Pedrosa will be looking to build on the momentum of his win in America last weekend, which moved him within 18 points of Yamaha's Lorenzo at the top of the standings.
He said: "Honda has been strong in the past few years here, so we hope to have a good performance in this race also. I'm looking forward to the race in Brno and to fight again for the victory."