Officials later confirmed that 98 overs, rather than the standard 90, would be scheduled for the second day in a bid to make-up lost playing time.
Malan was replaced by 20-year-old Ollie Pope, who is set to make his debut.
Uncapped Essex paceman Jamie Porter has been omitted from a 13-man squad, with England yet to decide whether Chris Woakes or spinner Moeen Ali will replace all-rounder Ben Stokes, who misses out due to his ongoing court case.
England lead the five-match series 1-0 after completing a thrilling 31-run victory at Edgbaston last week in Birmingham.
Powerful quake kills 82 on Indonesia's Lombok, tourists flee
Rescuers are still struggling to reach survivors of the deadly Indonesian natural disaster that has killed at least 91 people . The quake was so strong that it was felt even on the island of Bali , where like the rest of the American celebrity.
"When the wicket wears off, the spinners can come into play as well", Kohli said.
It proved beyond the tourists, despite Kohli making 51 to follow his first-innings 149 - the star batsman's maiden Test century on English soil.
"As long as we cross the line, that is the only thing that matters", Kohli insisted.
Other former India internationals to ring the bell at a Lord's Test are Sunil Gavaskar, The Nawab of Pataudi Jr, Dilip Vengsarkar, Rahul Dravid, Kapil Dev and Sourav Ganguly. "With the surface as it is, having looked at it today, we're going to leave it another 24 hours and then make a decision in the morning".
"Ollie Pope will bat at four", said Root.
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"I know that might be seen as quite a big jump". His form in the first Test proves him to be vital in the playing XI.
Yet this season has seen Pope make 684 runs for Championship leaders Surrey at an average of 85.5, including three centuries. Joe Root and his men would start confident thanks to their win in the first Test.
Ganguly, India's second most successful captain in Tests jointly with Virat Kohli at the moment, wrote in a column for the Times of India that India should seriously consider the option of fielding a second spinner at the iconic venue and also backed the chinaman ahead of the senior left-arm spinner.
"It's a good choice, a tough one too", Bharat Arun, India's bowling coach, told reporters at Lord's.
Strong quake again hits Indonesia's Lombok island
Emergency workers are continuing to dig through rubble and are gradually starting to reach more remote areas of the large island. With hospitals and clinics also affected, numerous injured have had to be treated in the open air or in makeshift clinics.