After a largely uneventful first half, Waterford made seven changes in the second half, bringing on Gavin Houlihan who gave the Blues the lead on 50 minutes when he finished off a pass from Izzy Akinade - Akinade himself headed over the bar 8 minutes later.
Dean O'Halloran went close on 67 minutes with a fine strike from 20 yards
Mark Stafford for Linfield equalised at 82 minutes after Matthew Connor had touched away a header from Matthew Clarke.
Stafford struck again scoring the winner in stoppage time from close range.
final score Linfield 2, Waterford FC 1.
Waterford FC's attentions now turn to a huge game in the RSC on Sunday when Shamrock Rovers come to town.
Stay tuned to WLR for all the build up to that match.