MATCH VERDICT: Double blow for league champions
Ashley Coddington's red card and a nine-minute hat-trick sent Moulton Harrox crashing to defeat.
The league champions looked on course for a double when Tom Panton and Declan Earth put them 2-1 up at half-time.
But two penalties by Jack Carter - plus a close-range header for his treble - allowed Whittlesey Athletic to regain control against 10 men.
Danny Maddison's spot-kick was too little, too late for Moulton as they couldn't force an equaliser in four minutes of stoppage-time.
The final on Saturday night had started perfectly as Earth set up Panton for a low finish.
However, Aaron Dunmore tapped in the leveller after Jamie Robinson pushed out Ricky Hailstone's free-kick.
Earth restored the lead for Harrox with a clinical strike just before the break and Marcus Parry hit the bar at the start of the second half.
The key moment came when Coddington was dismissed for a second bookable offence when he handled at the far post.
Carter converted and then made it 3-2 from the spot following substitute Matt Watkin's trip on Hailstone.
Ollie Long's corner was nodded in by Carter to open up a two-goal advantage.
Panton's volley bounced off the base of the post as Harrox tried to hit back with 10 men.
Further opportunities were wasted and a penalty appeal was rejected before Panton was fouled by keeper Johnny Pullan.
Maddison slotted home but Whittlesey completed a cup double to end Moulton's bid for more silverware.
4-2-3-1: Robinson; McGuire (sub Lambe-Hyner 78 mins), Coddington, Groves, Johnson; Maddison, Kisla; Parry (sub Watkin 55 mins), Townsend, Earth; Panton. Subs not used: Cairns, Price, Wilding.
5-3-2: Pullan; Long, Hailstone, Jenkins, Cook, Sansom; S Carter (sub Colbert 80 mins), Dunmore, Redhead (sub Quince 86 mins); J Carter, Heron. Sub not used: Glover.
Panton (17 mins, 1-0); Dunmore (28 mins, 1-1); Earth (43 mins 2-1); J Carter pen (55 mins, 2-2); J Carter pen (59 mins, 2-3); J Carter (63 mins, 2-4); Maddison pen (90 mins, 3-4).
Coddington (second bookable offence - handball).
Dunmore, Coddington, Pullan, Sansom (fouls); Long (dissent); Heron (unsporting behaviour).