Shipperley, who made more than 100 appearances for the Eagles during two spells at Selhurst Park, headed the decisive goal after 56 minutes.
Referee Iain Williamson awarded the goal to the Blades, despite furious protests from Gabor Kiraly, after ruling Shipperley's header had crossed the line.
Phil Jagielka, who netted twice in the 4-0 demolition of Luton in midweek, had taken his tally for the season to five in opening the scoring in the 15th minute and although Michael Hughes equalised seconds before the interval Paul Ifill's goal deep into stoppage time handed the advantage back to United.
Shipperley's goal put the visitors further ahead and although a Dougie Freedman penalty five minutes from time set up a tense finale the Blades held on.
After a tepid opening quarter of an hour the deadlock was broken following a dazzling run by Steve Kabba.
Kabba beat two defenders to get to the byline and cut the ball back for Jagielka to drive his low shot into the net via the post from close range.
Moments earlier Palace could have taken the lead through Freedman but his left-footed effort from the edge of the six-yard box came back off the woodwork.
Hughes thought he had sent his team into the interval all-square when he headed home Marco Reich's cross from close range for his first league goal of the season but Ifill had other ideas and restored the Blades' lead moments later.
Iain Dowie's side emerged from the break rejuvenated and Blades goalkeeper Paddy Kenny twice had to be at his best early in the second half to keep his side ahead, getting his fingertips to Ben Watson's curling free-kick before denying Tom Soares' effort from the edge of the area.
Emmerson Boyce then stung the palms of Kenny with a long-range drive as Palace looked for a reward for their pressure.
But it was the visitors who struck the decisive and controversial goal 10 minutes into the second half through Shipperley.
Freedman's fourth goal in as many matches, and his 99th in total for Palace, came after David Unsworth fouled Boyce and Marco Reich then saw his header cleared off the line by Jagielka right at the death.