"Brian has a long-standing chronic problem in his left knee and after the first one-dayer he pulled up a bit sore in that knee," team physiotherapist Stephen Partridge said in a statement on Tuesday.
"I have advised him to miss the second one-dayer," he added.
"The one-day form of the game puts far more pressure on his left knee than Test cricket, and with the World Cup around the corner he is heeding the advice of the medical team," Partridge added.
Vice-captain Chris Gayle will make his debut as skipper.
No decision has been taken on Lara's availability for the third and fourth one-dayers in Chennai (Jan. 27) and Baroda (Jan. 31).
All-rounder Dwayne Bravo has been declared fit for the match. He had sustained a shoulder injury when he collided with the square-leg umpire while fielding in the opening game.
Batsman Saurav Ganguly, whose masterly 98 in the first match last Sunday helped India end a six-game losing streak, has recovered from the cramps that prevented him fielding in the previous game at Nagpur.
"Saurav is fine...he bowled well and batted well so (it) should not be a problem," Dravid said, referring to Tuesday's net session.
The hosts have named their specialist spinners Harbhajan Singh and Ramesh Powar in the 12 for today's match with the pitch at the Barabati Stadium expected to turn.