The Nigerian defender had just one Capital One Cup appearance to his name this season having been sidelined since March with an Achilles injury.
But he powered home a second-half header to end Millwall's eight-game winless run and also halt Cardiff's winning start under new manager Russell Slade.
However Slade will be wondering how his City side, who are still winless on the road this season, did not take the lead late in the first half.
Instead Millwall were indebted to a stunning double save from former Bluebirds goalkeeper David Forde to deny Craig Noone and then, from close range, Adam Le Fondre.
Neither Forde nor opposite number David Marshall had been called into action for the majority of the half due to some wayward finishing from both sides.
Shaun Williams fired wide and Lee Gregory headed over for Millwall while John Brayford and Le Fondre sent presentable opportunities over the crossbar for the visitors.
But 10 minutes before the interval a slip in the Millwall defence saw the ball break to Noone on the left-hand side of the area.
The winger drove in a volley which Forde got down well to block, but only as far as Le Fondre who had what appeared a simple task to tap the ball into an empty net from all of six yards out.
However, Forde managed to spring back up and spread himself to deny the striker with his legs in spectacular fashion.
That save proved all the more vital nine minutes into the second half when Shittu, named captain on his return to the starting line-up, made the breakthrough.
Shaun Williams whipped in a corner from the right and Shittu rose above Bruno Manga and Federico Macheda at the far post to thump a downward header through a crowd of players and into the net.
Millwall could have added to their lead but Gregory lobbed over the crossbar when clean through and then missed the rebound after Scott McDonald's shot was parried, while Ed Upson drove wide from 15 yards.
Cardiff had a late penalty shout for handball against Shittu, after a mazy run from sub Ravel Morrison, waved away as the Lions held out for a much-needed win.
Sporting Life
