Joyce , the victim of a controversial run out on Sunday which saw former Afghanistan captain Mohammed Nabi receive a reprimand for an ICC Code of Conduct violation, took his own form of retribution on the Aghanistan attack.
The 37 year-old hit 19 fours and 3 sixes as he recorded the highest ODI score by any player on Irish soil.
He shared two significant stands - 134 in 176 balls with Gary Wilson, who showed a welcome return to form with a fine 58, and 71 in just 43 balls with Stuart Poynter.
Poynter's share was just 12 as Joyce abandoned his usual effortless grace for a more bludgeoning approach which saw 80 runs come from the final eight overs.
That saw Ireland post 265 for 5 - the highest score of the series.
Barry McCarthy and Peter Chase took two wickets apiece as the Afghan run chase stalled, but despite the required run rate passing double figures, the visitors were always in contention as Najibullah Zadran (54) and Rashid Khan (40) were at the crease.
Quick single for Sean Terry
However, having added 93, the pair were dismissed in quick succession as 212 for 6 became 212 for 9. Paul Stirling had Khan well caught by Kevin O'Brien , who then dismissed Mirwais and Najibullah in successive deliveries.
O'Brien - playing in his 100th ODI - finished with 3 for 59, to claim 10 wickets in the series.
Boundary for Ed Joyce brings up his hundred
Dalwat Zadran struck a few lusty blows in an unbeaten 31 as Afghanistan finished on 253 for 9.
Ed Joyce won Player of the Series for his 339 runs at an average of 169.50, pipping Rashid Khan and Kevin O'Brien.