Flood, who is expected to sign for Celtic, missed his second penalty of the sudden-death shoot-out as the Hoops won 11-10, to set up an Old Firm final.
Both sides had enjoyed strong spells in the goalless 120 minutes with Flood twice coming close and Georgios Samaras and Marc Crosas both hitting the United bar late in extra-time.
Celtic continued to have the upper hand after the restart and United needed Lee Wilkie’s sliding clearance as McDonald attacked a low cross from Samaras.
McDonald had a shot blocked in a crowded goalmouth before Samaras and Nakamura both shot into the side-netting from inside the box.
United came back into it in the second period. Flood skipped past Loovens after a one-two with Feeney but shot wide of the far post after Boruc came out to narrow the angle.
But the Tayside club twice had the woodwork to thank as they survived a late Celtic rally. Marc Crosas’ overhit cross sailed over Zaluska but struck the bar and Samaras headed against the bar from six yards following Robson’s cross before the final whistle signalled a penalty shoot-out.
Flood found the top corner with United’s first penalty and both sets of players, unable to score in 120 minutes, kept beating the goalkeepers.
The first 16 efforts were scored but with the scores tied at 8-8, Boruc dived to his right to save Wilkie’s low effort.
Loovens looked set to win it for Celtic but he shot straight at Zaluska, who blocked.
Kovacevic and Andreas Hinkel both netted to make it 9-9 before the goalkeepers, former Legia Warsaw team-mates and good friends, took their turn.
Zaluska found the bottom corner before Boruc coolly found the top corner.
Flood hit the bar with his second penalty before McDonald made it 11-10 and sent Celtic into the final.
CELTIC: Boruc, Hinkel, Caldwell, Loovens, Naylor, Nakamura, Scott Brown, Crosas, McGeady (Robson 75), McDonald, Vennegoor of Hesselink (Samaras 73).
DUNDEE UTD: Zaluska, Dixon, Wilkie, Kenneth, Kovacevic, Flood, Gomis, Buaben (David Robertson 90), Conway, Feeney, Sandaza (Daly 86).
Referee: C Murray.