It was the sixth time that Anderson has produced a five wicket haul at Lord's and he now has 99 Test wickets at the famous London venue.
James Anderson was on song in bowler-friendly conditions.
Anderson removed opening pair Murali Vijay (0) and Lokesh Rahul (8) before Pujara was sold short by his skipper in the ninth over as India fell to 15-3. A comic run out and almost three and a half hours of rain delay later, once again it fell to Virat Kohli to man the trenches against England's all out swing assault - once again his duel with Anderson demanded your attention.
In the first over back, Kohli, off strike, refused an easy single called by Pujara.
After a light shot to point from Pujara, Kohli began running to the unsafe striker's end, but soon changed his mind as he realised the risk of the situation.
Fans on social media were blowing up over Kohli's role in the dismissal.
Seasoned quick James Anderson took both the Indian wickets.
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England made a decision to handover a Test debut to the 20-year-old Ollie Pope for the second game of the five-match series against India.
Not even their woeful slip catching could hold England back, twice Jos Buttler dropped chances, twice he caught the same batsman the very next ball.
Off-spinner Ravichandran Ashwin (29) top-scored for the visitors even as the English pacers used the overcast conditions well, with Anderson emerging the wrecker-in-chief to pick 5/20.
It was another run out nightmare for Pujara to forget.
Woakes, who reached his century off just 129 balls, is playing in place of Ben Stokes, who was forced to miss the second test as he stands trial in a court in Bristol charged with affray.
With the forecast set fair for Saturday, it will be the turn of England's batsmen to drive home the advantage given to them by their bowlers on a day where there were two stoppages for rain spanning more than five hours.