The top placed Indians have five points from the first phase and will take on hosts UAE and Ireland, the second and third teams in group B, in the next phase.
The Indians dominated the game after winning the toss and rode on the fifties scored by three of their top five batsmen to put up a challenging total of 269 for Pakistan to chase.
Openers Uthappa (52) and Dhawan (52) gave India the perfect start, putting up a 100-run partnership, which was broken in the 16th over when Dhawan was stumped, foxed by a Mohammad Hafeez delivery. Dhawan's knock came in 51 balls and was studded with 11 fours.
His departure brought in skipper Venugopal Rao (45), who had no trouble in settling down but Uthappa was soon to join Dhawan in the dressing room, trapped leg before by Mansoor Amjad.
Rao was then joined by Rohit Sharma (62) and the duo steadied the ship and scored runs without taking too many risks. The two batted patiently to put up a fifty stand for the third wicket and took the total to 186 in the 36th over when Pakistan struck again.
Rao was removed by Hafeez just five runs short of his half century but Sharma carried on with support from Dinesh Karthik, who contributed a handy 33 runs to the innings.
Umar Gul finally got Sharma caught by Mohammad Irshad towards the end and India A scored 269 in their 50 overs at the loss of six wickets.
The Pakistani chase started on a disastrous note when opener Yaseer Hameed was trapped leg before by VRV Singh with the team score at 14 and were soon reeling at 53 for three, after losing the wickets of Hafeez and Amjad in quick succession.
Their innings were steadied by Bazid Khan, who along with opener Taufeeq Umar, took the score to 125 but just when the duo looked like taking the game away, Ravinder Jadeja struck and bowled Umar and then scalping the dangerman Khan at his personal score of 87.
RP Singh and Reetinder Singh Sodhi then teamed up to clean up the rest of the Pakistani batting line up, which collapsed after the dismissal of Khan and they eventually were all out for 235 as India A won the match with five balls to spare.