Gill and Kishan added 224 for the third wicket as India scored 402 after being put in to bat first in Lucknow on Wedneday.
Afghanistan could only reach 9-232 in reply, with Darwish Rasooli having to retire hurt.
After Yashasvi Jaiswal (4) had fallen early and Rohit Sharma (48) was bowled by Rashid Khan (3-48), Gill and Kishan kept the runs flowing, punishing the Afghan bowlers through the middle overs.
When India neared the 200-run mark, the two batters upped the tempo, scoring 121 in nine overs to get India to 2-307 after 36 overs.
Gill and Kishan both completed their centuries with boundaries in the 33rd over, while collecting 21 runs from Bilal Sami.
But spinner Nangeyalia Kharote (4-76) limited the damage, getting both of them out.
Kishan, who scored his first ODI century since 2022, hit seven sixes and 14 boundaries en route to an explosive 125 off 79 balls before getting caught trying to pull Kharote for six.
Gill was more measured, hitting only two sixes and 22 fours as he scored 154 off 110 balls, his ninth ODI hundred. But his tactful attempt to reverse sweep Kharote backfired, and the mis-timed shot got caught at deep point.
Kharote dismissed KL Rahul for a golden duck the very next ball, and India lost the rest of their batters within 42 runs, being bowled out with one ball to spare.
Rahmanullah Gurbaz, who'd scored a 48-ball century in the previous match, got dismissed at 41 by Gurnoor Brar (3-60) as Afghanistan set off on their massive chase.
Sediqullah Atal (42) failed to get the visitors back on track, and Rasooli had to retire hurt with a right hamstring injury soon after. Brar bowled captain Hashmatullah Shahidi two balls later.
By the time Arshdeep Singh (3-45) dismissed Rashid Khan and Allah Ghazanfar in two successive deliveries in different overs, it was all but over with Afghanistan at 190-7.
Only Rahmat Shah's lonely resistance, with a defiant 79 off 89 balls, helped the visitors get to 232 before the fall of their ninth wicket ended the match in the 45th over.
