Kelly's seat is a bright spot for Fine Gael
It proved a justification of the party's geographic-based three candidate strategy with Cork's Senator Deirdre Clune taking the fourth seat ahead of her running mate, Wicklow's Simon Harris TD, after a three-day count.
Sinn Fein's Liadh Ni Riada, a daughter of famed composer Sean O Riada, took the second seat.
Three of the MEPs elected are from Cork while the fourth is from Kerry.
No Leinster candidate was elected.
Fine Gael headquarters insisted on running three candidates drawn from strategic parts of the vast Ireland South constituency which stretches from west Cork to Wicklow and from Wexford to north Clare.
"It was not easy because of the scale of the constituency and the way it was divided up. It is a crazy size. I'm just so grateful for the way people supported me," former GAA president Mr Kelly said.
In a fitting twist, Mr Kelly officially opened the Nemo Rangers clubhouse in Cork, where the Ireland South Count took place, in 2005.
Fine Gael celebrated winning the two seats after Senator Clune, the daughter of former Tanaiste Peter Barry, narrowly managed to stay ahead of Mr Harris and win the final seat by 3,562 votes (Clune 74,370 to Harris 70,808), on the 12th count.