MK Dons missed two penalties but snatched a late draw through Gareth Edds' 20-yard injury-time strike.
Izale McLeod put MK Dons ahead with his right foot but missed a penalty kick after a handball by Paul Morgan.
Jamie Forrester equalised from the spot after Dean Lewington handled and substitute Spencer Weir-Daley slotted home what looked to be a late winner.
Morgan then saw red for a foul on McLeod but Aaron Wilbraham hit the crossbar before Edds' last-gasp strike.
Milton Keynes Dons: Harper, Edds, Diallo, O'Hanlon, Lewington, McGovern (Stirling 81), Andrews, Mitchell (Platt 62), Dyer (Gary Smith 76), Wilbraham, McLeod.
Subs Not Used: Baines, Taylor.
Goals: McLeod 6, Edds 90.
Lincoln City: Marriott, Beevers, Morgan, Mayo, Kerr (Moses 82), Frecklington, Brown, Amoo, Hughes, Forrester (Weir-Daley 82), Stallard.
Subs Not Used: Rayner, Gritton, Kell.
Sent Off: Morgan (90).
Booked: Frecklington.
Goals: Forrester 51 pen, Weir-Daley 84.
Att: 7,140
Ref: R Booth (Nottinghamshire).