Rob Duffy's injury-time penalty fired Mansfield to victory as Rushden dropped down to fifth in the table.
Diamonds striker Aaron O'Connor fired home from 25 yards against his former club to opening the scoring but Jake Speight replied from a similar range.
Jefferson Louis set up Sam Smith for Rushden's second before Speight calmly lobbed Dale Roberts for 2-2.
Louis was sent off for a second booking and Mark Byrne brought down Kyle Nix for Duffy's converted penalty.
Rushden & Diamonds manager Justin Edinburgh told BBC Radio Northampton: "There were countless errors and big calls that have gone against us.
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"We haven't lost that game, we were beaten by the man in the middle.
"We were outstanding in the first half, with some very good play.
"We gifted them the opportunity to get back in the game and then some decisions didn't go our way and we've lost the game.
Mansfield: Marriott, Silk (Istead 67), Foster, Garner, Nicholas, Briscoe, Mills, Nix, Burgess, Perry (Duffy 54), Speight. Subs Not Used: Collett, Somner, Shaw.
Booked: Silk, Istead, Speight, Duffy.
Goals: Speight 48, 77, Duffy 90 pen.
Rushden & D'monds: Roberts, Huke, Osano, Stuart, Robinson, Byrne, Terry, Pattison (Porter 74), Louis, O'Connor, Akurang (Smith 68). Subs Not Used: Day, McNamara, Beecroft.
Sent Off: Louis (84).
Booked: Louis, Akurang.
Goals: O'Connor 16, Smith 71.
Att: 2,031
Ref: Jeremy Simpson (Lancashire).
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