Opening batsman Gambhir and Dhoni shared a 207-run second wicket stand as the Indians rattled up a mammoth 330 for six after being sent in by Pakistan skipper Misbah-ul-Haq at the Nairobi Gymkhana Club ground.
In reply, Pakistan 'A' was all out for 209 in 44.5 overs.
Gambhir slammed 122 off 113 balls with 10 fours and three sixes while wicketkeeper batsman Dhoni was equally aggressive during a 122-ball 120 studded with 10 fours and two sixes.
Ramesh Powar than struck a whirlwind 33 that came off only 19 balls and contained four boundaries and a six.
Iftikhar Anjum was the only bowler treated with respect and he finished with a fine spell of 4-44.
The Pakistan chase was never off after they lost opener Shadab Kabir off the first ball of the innings, caught by Dhoni off right arm seamer Amit Bhandari.
Bhandari went on to claim 3-53 while his new ball partner Shib Sunder Paul and Powar picked 2-39 and 2-33 respectively.
The 63-run second wicket partnership between Taufiq Umar (26) and Bazid Khan (44) was the only bright phase of the Pakistan innings although Qaiser Abbas (58) provided a late spark adding 51 for the ninth wicket with Mansoor Amjad (33).