Mohali : Indian bowlers claimed two wickets at the fag end of the day to reduce England to 282/6 at stumps on the third day of the second Test at the PCA stadium in Mohali on Sunday.
Mishra struck on the last ball of the day when he had Flintoff (62) caught brilliantly by Gautam Gambhir at forward short leg. The burly England all-rounder hit 6 fours and a six in his knock.
In the over before that, Harbhajan ended Pietersen's excellent innings by dismissing him leg before wicket to reduce England to 280/5.
England still trail India by 171 runs with four wickets in hand in their first essay. Pietersen had hit his 15th Test century and become the third fastest England player to reach 4,000 Test runs on 105, beaten only by Herbert Sutcliffe and Len Hutton.
He hit 17 fours and a six during his brilliant 144 and transformed England's fortunes with his aggression, only for India to fight back in the closing overs.
Left-arm seamer Zaheer Khan had undermined England's reply with the third ball of the innings when he won an lbw appeal against Andrew Strauss.
England slipped into further trouble in the next over with seamer Ishant Sharma continuing Ian Bell's struggles by removing his middle stump with his first delivery.
India captain MS Dhoni used Pietersen's arrival at the crease to embark on psychological tactics to try to unsettle his rival.
Instead of continuing with Zaheer following his successful first over, Dhoni turned to the occasional left-arm spin of Yuvraj Singh, who has waged a running battle with Pietersen through the series.
It was a tactic which was almost inspired with Pietersen nearly bowled off an inside edge from the first delivery, while he almost picked out extra cover with a drive off the final ball of the over.
Yuvraj was taken off after one over and it took the return of Zaheer midway through the afternoon session to make the next breakthrough, an inswinging yorker accounting for Alastair Cook lbw for 50 - his 20th innings without a century.
But with Flintoff showing aggression from the start of his innings, England quickly regained the momentum and added 154 runs in the afternoon session.
It prompted India to go on the defensive and bowl way outside off-stump for most of the final session, and it paid off in the closing minutes when Harbhajan won an lbw appeal against Pietersen.
England chose to use nightwatchman James Anderson rather than send out Matt Prior but it backfired when the Lancashire seamer took a single in what became the final over of the day to expose Flintoff, who gave a bat-pad catch to short leg off leg-spinner Amit Mishra.