Matt Shanahan defeated independent abortion rights campaigner Claire Cullen Delsol by 25 votes to 5.
The Health Equality for the South East spokesperson received support from Fine Gael, Fianna Fáil, Labour and independents, while his opponent was backed by Sinn Féin members.
The seat had been vacated by Mary Roche, who resigned last November citing personal circumstances.
Her former independent colleagues, Davy Daniels and Cha O'Neill proposed and seconded Matt Shanahan.
Sinn Fèin's Breda Brennan and Siobhàn Whelan nominated Claire Cullen Delsol.
Fine Gael's Damien Geoghegan says that if Councillors voted for a candidate other than Mary Roche's chosen replacement, it could lead to adverse consequences in future co-options.
Fianna Fàil voted for Matt Shanahan, but Cllrs Eddie Mulligan and Adam Wyse commended Ms Cullen Delsol for putting herself forward.
Matt Shanahan told WLR News after the vote that he wants to use the position to promote cardiac care at University Hospital Waterford.
