The colts, under head coach Colm Toal Joseph, came back through Daniel Lalhlimpuia in the 28th minute after being a goal down in the 16th minute of the match when their opponents scored from the spot.
But UAE found the back of the net in the 36th minute to gain the upper hand one more time. An eventful first half was followed by a goalless second half.
The Indian team will play the same opponents in the third and last friendly on Friday before heading into the tournament which starts September 22.
The Indians earlier beat U-17 Al Kaleej Academy 4-1 in the first friendly. India have been clubbed in Group D with Uzbekistan, Syria and China in the final phase. India play Uzbekistan in their first match on September 23.