Andrew Strauss, vying for a place in the side with Shah, was out hit wicket to Mark Gillespie for only four.
He played a defensive shot against seamer Gillespie and, in attempting to prevent the ball from rolling back onto the stumps, hit his wicket.
After Gayle's appeals for lbw were turned down by Saheba, the West Indies skipper called for a second opinion and Rudi Koertzen decided the ball would have hit the wicket after watching TV replays, ending Flynn's resistance on 95.
The visitors were hit by injuries to wicket-keeper Nic Pothas (calf strain) and his replacement Michael Brown (damaged finger).
As wickets fell at the other end, Cheema stepped down the wicket to hit another six, this time off Mendis, but in doing so broke his bat and was caught slog sweeping next ball, which ended hopes of a famous victory.
Boje claimed the wicket as Gallian hit him straight down Rob White's throat at mid-on.
Waingankar then claimed the key wicket of Kevin Pietersen, who advanced down the wicket trying to whip the ball through mid-wicket but was hit on the pad - and the umpire upheld the lbw appeal.
In addition to his first ball wicket on Sunday he hit a brisk 40, batting at number 11 in the first innings.
Kent hit back with a sixth-wicket stand between Van Jaarsveld and Alex Blake, but Ashraf rejoined the attack to deny Van Jaarsveld his century.
Mike Hussey, Brad Haddin and Mitchell Johnson all hit fifties before a last-wicket stand of 35 between Peter Siddle and Ben Hilfenhaus boosted the total.
England badly needed a partnership and Matt Prior, though struggling to time the ball at first, added crucial runs with Paul Collingwood, who hit a six over mid-wicket as 23 came in the two batting powerplay overs.
Yasir Arafat returned to bowl John Maunders but James Middlebrook hit a six over mid-wicket off a slower ball from Azhar Mahmood in the 38th over, to ease the pressure on Essex, who took eight from the penultimate over to ease home.
Kieswetter's luck ran out when he called for a suicidal run having hit straight to short mid-wicket, Kevin Pietersen rightly refused and the wicketkeeper-batsman was given out after lengthy video referrals which finally concluded his bat had bounced into the air when he dived for his crease as Niall O'Brien whipped off the bails.
Pietersen helped reduce the requirement to 44 from 38 before he mis-cued to deep mid-wicket, but Flintoff somehow hit some more awesome shots as England achieved a relatively comfortable win in near darkness, despite some regrettable delaying tactics from the South Africans.
The Western Australian put on 57 for the second wicket with Samit Patel, who hit Steven Croft over cover for six before he was removed for a confident 31 by leg-spinner Simon Marshall, edging a sweep to wicketkeeper Gareth Cross.
Chris Cairns and Chris Read quickly followed as the run-rate slowed in the middle overs, with Voges pulling Du Plessis to the waiting Flintoff at deep mid-wicket, leaving Mark Ealham to hit two sixes in a late cameo of 28 off 21 balls.
Botha scored 42 while wicket-keeper Niall O'Brien hit 72 as the hosts made 222-7 batting first.
BBC: SPORT | Cricket | International Teams | Botha stars as Ireland beat Scots
Wicket-keeper Mustard, who had hit some thunderous shots over the infield in the Twenty20 matches, was deprived of leg-side hitting opportunities.
Wicket-keeper Mahendra Dhoni, who hit 92 from 81 balls, said India would have to work hard to secure a victory, despite taking a 640-run first innings lead into day three.
England seemed certain to lose by an innings, but Broad hit the ball so sweetly in a defiant last-wicket stand.
Both players hit boundaries but Pothas holed out to deep mid-wicket for 47 and Mascarenhas was bowled by England's Liam Plunkett, who impressed with 3-42.
Malan shared 143 for the third wicket with England captain Andrew Strauss, who hit 69, as Middlesex closed on 187-4 after being set 375 to win.
South Africa lost Hashim Amla cheaply at the start of their reply and Gibbs was caught on the mid-wicket boundary for 19 when he tried to hit Hopes over the top.
The stage was set for Pietersen to hit the winning runs, perhaps with a switch hit, but after one memorable whip through mid-wicket for four, he was out rather tamely, caught at short-leg off bat and pad.
The left-hander hit three quick fours making Ntini opt to go around the wicket, and when a shorter delivery seamed away from Hayden a thick edge flew to captain Graeme Smith at first slip.
Tim Bresnan, who hit 36 in a stand of 80 with Bell for the eighth wicket, first removed Ed Cowan for 33.
West Indies were 35 for no wicket when play ended with opener Chris Gayle, who hit 154 in the first innings, nine not out and Wavell Hinds on 22.
He faced 184 balls and hit only nine fours, but his contribution to a sixth-wicket stand worth 81 in 26 overs with Gareth Batty was instrumental in avoiding the follow-on.
In his second Test, Jaques hit 66 before miscuing a sweep off spinner Mohammad Rafique to mid-wicket.
Hildreth and Compton stayed together to add 76 for the fourth wicket before Hildreth became Kaneria's second victim when he hit the ball straight to cover.
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