The Blues couldn't repeat their Johannesburg heroics despite late consolation tries to Rieko Ioane and Moala.
Strong performances from Perofeta, George Moala and Northland's Josh Goodhue were rare highlights in a poor performance that dents their finals aspirations.
The Blues found their attacking mojo in the second spell, scoring thrice inside the first 15 minutes of the half before added a pair of consolation efforts in the dying minutes.
Of particular note was the Blues propensity to concede penalties within the arc of du Preez's educated boot. He punished the Blues to the tune of seven penalty goals of varying difficulty.
Earlier the Blues barely fired a shot in a messy first half as ill-timed penalties and handling errors pinned them inside their own half.
Both of the Sharks tries came via uncommitted defensive stops from the Blues as captain Ruan Botha and impressive flanker Jean-Luc du Preez eased their way through a defensive line that at times resembled an automatic door.
When the Blues finally got in attacking territory they found their way over the line as Goodhue featured twice in a series of offloads that set up a major overlap, paving the way for a Michael Collins try.
Goodhue and fellow Northlander Sam Nock both enjoyed industrious efforts with Goodhue in particular impressing with his work ethic in his first Super Rugby start.
Prop Ross Wright and flanker Kara Pryor gave good impact from the bench but were unable to lead a second Blues comeback.
The Blues are in must-win territory when they take on the Chiefs in Hamilton next Saturday.
Sharks 63 (Ruan Botha, Jean-Luc du Preez, Lubabalo Mtembu, Robert du Preez, Kobus van Wyk, Curwin Bosch tries, Robert du Preez 6 con, 7 pen)
Blues 40 (Michael Collins, Akira Ioane, Patrick Tuipulotu, Stephen Perofeta, Rieko Ioane, George Moala tries, Perofeta 4 con, Bryn Gatland con)
Halftime: 26-7
