Bakary Sako's free-kick put Wolves ahead after 10 minutes, but Whittingham brought the Bluebirds level a minute later from the penalty spot.
He then scored his second shortly afterwards from the edge of the box to give the hosts the lead after 14 minutes, before completing his hat-trick in the 65th minute with a free-kick.
New signings Nicky Maynard and Craig Noone made their Cardiff debuts on an afternoon that indicated the Welsh club could be in for a successful season.
They replaced Don Cowie and Aron Gunnarsson in the starting XI as Malky Mackay's side lined up in a 4-4-2 formation. Another recent arrival, Tommy Smith, made his first home start.
Meanwhile, South Korea international Bo-Kyung Kim was on the bench for the first time after receiving international clearance.
Wolves boss Stale Solbakken changed all 10 outfield players, with goalkeeper Carl Ikeme the only survivor from the Capital One Cup victory at Northampton on Thursday night.
Cardiff created the first chance as Noone's piledriver was palmed upwards by Ikeme after Wolves failed to clear a Whittingham corner.
At the other end Sako deceived Cardiff goalkeeper David Marshall with a curling free-kick to put Wolves in front after Whittingham pushed over Sylvan Ebanks-Blake in the inside-right position.
But the hosts were immediately level. Ronald Zubar was off balance and left a leg dangling for Noone to fall over. It was a clear penalty and Whittingham calmly stroked his kick low down the middle as Ikeme dived to his right.
Whittingham then struck from 20 yards as Cardiff completed a quick turnaround after falling behind.
Only a fine fingertip save from Ikeme denied Whittingham his hat-trick early in the second half.
Wolves should have equalised when Zubar climbed highest to reach Stephen Ward's cross but he headed over the crossbar.
Whittingham made them pay, sending his free-kick into the top left-hand corner after Noone had been fouled by Tongo Doumbia on the edge of the box.
Heidar Helguson, Smith and substitute Cowie all threatened to extend Cardiff's advantage, but were unable to add a fourth.
It mattered little, though, as Wolves were thoroughly disappointing and created little else. Goalscorer Sako had an effort from just inside the area blocked by Matthew Connolly late in the game but that was as good as it got.