Rahul, who missed the first Test triumph due to viral fever, maintains an impressive average of 44.44 in 17 Tests for India.
India outplayed the hosts by a record 304 runs in Galle, with openers Shikhar Dhawan and Abhinav Mukund putting in strong performances at the start of the three-match series.
Speaking on the eve of the Colombo Test, Kohli made it clear that despite their stellar showing, one of the two openers will have to make way for Rahul, who is known as KL.
"Obviously KL has been our established opener. I feel one of the openers will have to make way for KL," Kohli said of the 25-year-old.
"What he's done in the past two years for us has been very solid, and he deserves to come back and start fresh in Test cricket again."
Dhawan hit a brilliant 190 in India's first innings in Galle and is expected to retain his spot. That means Mukund is likely to miss out despite a gritty 81 in the second innings.
Rahul, who has hit four Test centuries and seven fifties, played a vital role in India's series win over Australia in March despite getting injured during the first match.
"He has batted really well in the last couple of seasons for us. As I said, it is very important for us to make him feel that this is his spot," said Kohli, who gave no other details on the playing XI.
Top-ranked India are looking to seal the series at the Sinhalese Sports Club Ground against Sri Lanka who will welcome back skipper Dinesh Chandimal after a bout of pneumonia.
Indian coach Ravi Shastri has talked up his team's abilities, saying on Tuesday (1) "a lot of big names have played for 20 years and they have come to Sri Lanka many times but they have never won a series. This team has done that."
India overturned a 1-0 deficit to beat Sri Lanka in 2015 and register their first Test series triumph in the island nation for 22 years.
India reclaimed the world number one Test spot from arch-rivals Pakistan last year.
