Besides skipper Virat Kohli, the franchise retained 13 others, including former Protea captain AB de Villiers and New Zealand quick Tim Southee.
Woakes picked up three wickets in the morning session to negate India's solid start. Thereafter, Virat Kohli and Ajinkya Rahane put on 159 runs partnership.
However, just when India had hoped for them to continue the good work and convert this into a massive partnership, Rahane was dismissed by Stuart Broad.
The home skipper hailed his team's bowling performance, which handed them a 2-0 lead in the five-match series.
England beat India at Lord's in the second Test by an innings and 159 runs to take a 2-0 lead in the five-match series.
India suffered an embarrassing 159-run innings defeat in the second Test against England after yet another batting failure on day four at Lord's.
Live Cricket Score, India vs England, 2nd Test, Day 4: Catch all latest updates, live score and ball-by-ball commentary from Day 4 of the second Test between India and England at Lord's on IndiaTV Sports.
Woakes had recently become a father and said that his teammates had asked him to do a "baby celebration" but it all became a bit of blur once he achieved the coveted landmark.
Woakes struck his first Test century to guide England to 357/6 and a commanding 250-run lead over top-ranked India.
Coming in on the sixth wicket, Woakes and Bairstow tore apart the Indian bowling unit with their 189-run partnership, with the pacer going on to score his maiden Test century.
Woakes was batting on 120 while Sam Curran was unbeaten on 22, as the home team extended its first-innings lead to 250 runs with four wickets remaining at the Lord's.
While skipper Virat Kohli had insisted that there are no technical problems but the horrendous batting effort painted a sorry picture.
Stokes misses out on the 2nd Test as he faces a court hearing in Bristol after he was involved in a brawl last year, whereas Malan has been dropped after he failed to make an impact in the Birmingham Test.
Stokes was sidelined for the first two games of the five-match series, both won by England, due to a torn left hamstring.
Pakistan didn't capitalize on winning the toss at Headingley, with its batsmen failing to handle a swinging and seaming ball as England's pace attack dominated the proceedings on Day 1.
Sydney: Already out of the World Cup, England on Wednesday suffered further blows with all-rounders Chris Woakes and Moeen Ali being ruled out due to injury for their final and inconsequential Pool A encounter against
Sydney: Chris Woakes snared five wickets to restrict West Indies to 122 before England cruised to a nine-wicket victory in a World Cup warmup match on Monday.Woakes (5-19) tore through the top order, dismissing Chris
Sydney: Chris Woakes completed a five-wicket haul as England dismissed the West Indies for just 122 in the 30th over of a World Cup warmup match on Monday.Woakes tore through the top order, dismissing Chris
Sydney: England's World Cup preparations suffered an early setback Friday when it was beaten by three wickets by Australia in the first tri-series one-day cricket international.Opener David Warner crashed 127 from 115 balls to drive
London: England Monday announced a 15-man squad to face India in an ODI series with T20 specialist Alex Hales getting a call-up to the national team. Hales appears set to become captain Alastair Cook's new
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