Bad light has forced the umpires to call off the play for the day. India were 107 all-out in just 35.2 overs.
He targeted Ravichandran Ashwin, scooping him over the wicketkeeper's head and flogging him over cow corner for four as he neared three figures.
Both Kohli and Rahane survived the early jitters from the English pacers to start the rebuilding work with a 34-run fourth wicket stand before the in-form India captain fell to Chris Woakes.
Chris Woakes' maiden Test century put England in total control on the third day of the second Test against India.
Before this series, KL Rahul's previous Test innings against England brought him 199 at Chennai in December 2016.
The all-rounder's unbeaten 120, coupled with 93 from Jonny Bairstow, took the hosts to 357-6, a lead of 250.
"I would be so disappointed if I had messed up today because they were ideal conditions to bowl in".
In the first match at Edgbaston in Birmingham, he scored 149 runs in the first innings followed by a gutsy knock of 51 runs.
After a delay of more than two hours, the players returned for 12 balls, during which Kohli and Pujara groped around trying to find the ball as Anderson and Stuart Broad terrorised them under leaden skies.
Even Kohli failed to make an impact, scoring just 23 runs.
With the sun shining it looked like flawless batting conditions, but the rare rainfall of the previous two days in London still gave the India attack hope they could bowl their side back into he match.
That brought in new cap Ollie Pope.
As expected England gave a Test debut to 20-year-old Surrey batsman Pope, who has competed in only 15 first-class matches but takes the place of the dropped Dawid Malan. He got off the mark with a four and looked composed throughout out his innings of 28 before he was LBW to Hardik Pandya (one for 16).
India captain Virat Kohli may field the same playing XI for two consecutive Test matches for the first time since he took over as captain in the longer formats in 2014. The wicket offered the bowlers something, he outscored Joe root at the other end and so far at least it is the best score of the match.
That easy wicket for England left India at 3/15.