Pietersen will be sidelined for six weeks after surgery on an Achilles injury which had troubled him throughout the first two Tests.
The 29-year-old batsman, whose highest score in the series was just 69, had hoped pain-killers would allow him to help England build on the 1-0 lead they earned at Lord's this week.
But the injury, which first occurred against the West Indies [ Images ] earlier this year, deteriorated during the five-day clash and Pietersen agreed with advice from a specialist to have immediate surgery.
Now Andrew Strauss's [ Images ] side face the prospect of heading into the third Test at Edgbaston next week on a low despite their impressive Lord's performance.
Flintoff, who is struggling with injury problems of his own, conceded Pietersen's injury may give the Australians a major boost.
"He's a massive influence on our team so it's going to make it tougher for us - but he's been in pain," Flintoff said. "He will be greatly missed and we wish him well - he'll be gutted."
"He's performed well in the past and we expected him to in the next three matches but he'll come back, he's young and I'm sure he's got a few more Ashes series in him yet.
"If (Australia captain) Ricky Ponting [ Images ] was injured you are quite happy not bowling at him - and I think Australia will be thinking the same about Kevin.
"It means a lot playing in the Ashes and I fully expect he'll be coming along to watch a few of the games once he's back on his feet," said Flintoff.
Flintoff added: "Ian Bell has been playing well for Warwickshire but whoever comes in we have to move on pretty quickly and get our bodies and minds right for the Test next week."
Only 24 hours before his operation, Pietersen had spoken of his determination to follow Flintoff's example and play through the pain barrier.
Despite pain from a knee injury that has forced him to announce he will retire from Test cricket after the Ashes, Flintoff took five wickets in the second innings to kill off Ricky Ponting's men.
Pietersen wanted to perform similar heroics but has been forced to accept defeat.
"As an England cricketer the Ashes are the pinnacle of the game so I'm absolutely devastated to be missing the rest of this series," he said.
"Up until now the Achilles injury has been manageable but it recently reached the point where we needed to look at other options in terms of treatment.
"I hate missing matches for England and especially during an Ashes summer but now that the decision has been made to undergo surgery I'm confident I can return to the England team injury-free following a course of rehabilitation.
"Unfortunately the injury has recently deteriorated. To leave a winning dressing room at this time is heart breaking but it wouldn't be fair to the team or myself to continue given the severity of the injury.
"I'll be supporting the team closely and wish them the best of luck as they look to build on the brilliant win at Lord's and reclaim the Ashes."