Afghanistan bowled out for 116 after Chameera takes four
Leg-spinner Wanindu Hasaranga polished off the Afghan tail with 3-7 in Hambantota.
The fast bowler Chameera, returning after ankle surgery that sidelined him for seven months, finished with figures of 4-63.
He was ably assisted by two wickets from fellow quick Lahiru Kumara, who withdrew from the first ODI with a hamstring strain.
Mohammad Nabi's 23 was the top score of the Afghan innings as the tourists failed to post a decent partnership, with Sri Lanka taking wickets at regular intervals.
Afghanistan, who had opted to bat first, won the first ODI by six wickets. Sri Lanka bounced back to win the second game by 132 runs.
Sri Lanka will be heading to Zimbabwe straight after this series for World Cup qualifiers in a bid to secure one of the two remaining slots for the format's showpiece event.
Afghanistan are already through to the World Cup, to be held in India from October.