Rahane, who has been in wretched form for the past couple of years and also had a poor county stint with Hampshire, was out for 1, edging seamer all-rounder Jonathan Carter behind stumps to keeper-captain Jahmar Hamilton.
The dogged Cheteshwar Pujara was batting on 16, having faced 51 balls alongside Rohit Sharma, who got a few crisp boundaries to remain unbeaten on 22 off 38 balls.
Earlier, KL Rahul looked fluent during his knock of 36 off 51 balls with five fours and a six but fellow opener Mayank Agarwal's (12) defence was breached within the first hour.
Rahul looked good for a big one before being holed out to Romario Shepherd off new ball bowler Keon Harding's bowling.
The talking point of Indian batting has been Rahane, who has gone without a hundred for the past two years. His last three-figure knock came against a below-par Sri Lanka side in August 2017.
In the last 12 Test matches, he has crossed half-century mark only five times in 20 innings.
His place in the playing Xi is not under threat at least for this two-Test series but the same can't be said for the home series against South Africa and Bangladesh at home if he happens to fail in the current series.
With Hanuma Vihari closing in on him and Shreyas Iyer waiting in the wings, it's a tense time for the Indian vice-captain.
Brief Scores:
India 1st Innings (at Lunch): 89/3 (KL Rahul 36, Mayank Agarwal 12, Cheteshwar Pujara 16*, Rohit Sharma 22*; Jonathan Carter 2/24 in 9 overs).