India A made 224 for four batting first, but it was the weather that provided the sternest test, with temperatures plummeting to uncomfortable levels at the Palam Services Ground and low-lying fog causing bad light and a reduction off 11 overs per innings. Murali Vijay was the hosts' top-scorer with 76, while Jade Dernbach picked up two wickets at the end.
England opted for Jos Buttler ahead of Joe Root, with Stuart Meaker and Danny Briggs the others to miss out.
In Cook's absence Eoin Morgan led the side, winning the toss and opting bowl first, but after a delayed start the game was again interrupted by bad light with the score at 15-0 after five overs. The players were off for over an hour but eventually re-emerged.
Steven Finn had a strong lbw shout against Murali Vijay with his second ball after the restart but did not persuade the umpire and then saw his next delivery nicked for four. Tim Bresnan replaced Dernbach following a tight opening spell and shipped 20 in his first three overs, with Vijay cashing in through the off side.
Home captain Abhinav Mukund picked up his scoring rate too, scoring predominantly in the third-man region as the hosts reached 75 after 15 overs.
Vijay then went after Chris Woakes in the 17th, chipping him for three over the top and then striking a clean six down the ground. Both batsman passed 50 looking relatively untroubled, with 106 on the board at the end of the 20th over.
Off-spinner James Tredwell eventually struck for England with the score at 118, Mukund falling stumped for 57. Vijay carried on the fight, lifting Tredwell for a straight six and a reverse-swept four.
He was gone for 76, Samit Patel rocking back his leg stump with a quicker delivery, but Ashok Menaria picked up the baton with successive maximums off the England all-rounder.
Menaria reached 17 before he mis-timed a pull and was caught by Kevin Pietersen off Dernbach's bowling. Dernbach also saw off Jalaj Sexena for two, with Kedar Jadhav scoring unfussily at the other end, reaching a tidy 52 not out by the end of the innings.