Getting behind a 338-run lead, India lost Murali Vijay for 2 after pace spearhead James Anderson (1-1) trapped him LBW in the fifth over of the innings.
A struggling Gautam Gambhir threw away his wicket after the left-hander fell short of his ground at the non-strikers end when a direct throw from Chris Woakes sent him back for 3.
Heavens soon opened up as the umpires called for early lunch with Cheteshwar Pujara unbeaten on nought as India trail by 329 runs.
Earlier starting on their overnight score of 385 for seven, the hosts managed 486 in 116.3 overs, courtesy Root's unbeaten 149 as Indian bowlers once again struggled for line and length on a cloudy morning.
Ishant Sharma picked up the wickets of Chris Jordan (20) and Stuart Broad (37) to end up with figures of 4-96. Off-spinner Ravichandran Ashwin (3-72) wrapped up England's innings after trapping Anderson LBW for 1.
With an extra wire on his helmet grill to protect his injured nose, Broad played a crucial cameo as he was consistently treated with bouncers by the Indian pacers.
The eight-wicket 82-run partnership between Jordan and Root and the 63-run ninth wicket stand between Broad and Root were the highlights of the morning session before the fall of the two Indian wickets.
India, who were shot out for 148 in 61.1 overs in the first innings, have still not learnt their lessons and will certainly have to pull a rabbit out of the hat or pray for the weather Gods to help them save this game.