Jim Bentley’s players had trailed to Richard Brindley’s first-half goal before Antony Evans was sent sprawling inside the area on 88 minutes.
Having missed his last spot-kick, Rose kept his cool to send Sam Walker the wrong way from 12 yards.
After winning at Stevenage on Good Friday, the Shrimps were unlucky to be behind at half-time after matching their visitors in the opening 45 minutes.
A belated offside flag cut short Kevin Ellison’s celebrations after he had bundled the ball home, while Paul Mullin fired over when well placed.
The opening goal came midway through the first half when Alex Whitmore fouled Tarique Fosu 25 yards out and Brindley’s curling free-kick gave Danijel Nizic no chance.
In contrast, the second half was much scrappier with chances at a premium as Alex Kenyon fired into United’s side netting, while Tom Eastman volleyed a corner wide of Nizic’s goal.
Although Bentley rang the changes, it looked to be in vain until Rose’a dramatic intervention.
Morecambe: Nizic, Whitmore, Winnard, Kenyon (Murphy 83), Duckworth, Fleming, Rose, McGowan, Wildig (Evans 46), Mullin, Ellison (Turner 79). Subs not used: Maher, Wakefield, Molyneux, Conlan.
Colchester United: Walker, James, Eastman, Elokobi, Brindley, Loft (Wynter 76), Murray, Drey Wright (Pyke 90), Dickenson, Porter, Fosu (O’Sullivan 83). Subs not used: Brill, Briggs, Kinsella, Diaz Wright.
Referee: Sebastian Stockbridge.