Summer signing Caulker, who spent the 2011/12 season on loan at Swansea, rose to head home Craig Bellamy's 62nd-minute corner at the Cardiff City Stadium after Jonjo Shelvey moved away from his covering position on the post.
Swansea's day was further soured when goalkeeper Michel Vorm was sent off in stoppage-time after taking out Fraizer Campbell as the Cardiff striker broke clear.
Moments before Vorm's red card, his opposite number David Marshall saved from Jonathan de Guzman and Alejandro Pozuelo as Swansea stepped up their search for an elusive equaliser.
Full-back Angel Rangel was forced to don for the gloves for the final stages after Vorm's dismissal and he saved well from Peter Whittingham's free-kick as Cardiff held out to celebrate a first home win in over two months.
Swansea had looked to control possession amid the deafening noise of the opening exchanges, and they carved out a great opportunity in just the fifth minute.
Michu brilliantly controlled Shelvey's cross but, having done the hard part, volleyed well over the bar.
The Spaniard then warmed Marshall's hands from distance as Swansea started with the greater authority.
The expected on-field hostilities soon arrived as Rangel and Bellamy exchanged words as it took Cardiff time to settle, but Ben Turner's strong challenge on Shelvey sparked a gradual change in proceedings.
As predicted, Cardiff threatened at set-pieces, and Leon Britton came uncomfortably close to diverting a Bellamy free-kick into his own net.
A couple of pin-point dead-ball deliveries from Peter Whittingham forced Vorm to punch unconvincingly and, as Cardiff got a foothold in midfield, the action dried up.
Swansea enjoyed the better of possession, but Cardiff were comfortably able to soak it up, while reluctant to press on in attack and the arrival of the half-time whistle was almost merciful.
There was at least a modicum of action early in the second half. Peter Odemwingie narrowly failed to connect with a Caulker flick-on, before Whittingham drove wide following a purposeful surge from Kevin Theophile-Catherine.
The Bluebirds had half-hearted penalty appeals for a foul on Don Cowie by Ashley Williams turned away by Mike Dean, refereeing in the Welsh capital for the first time since being struck by a coin in this fixture over four years ago.
But they got their reward for their strong start to the second half in the 62nd minute, and it was Caulker who stung his former club.
The England defender rose above Chico Flores, the man Swansea signed to replace him following the end of his loan spell at the Liberty Stadium, to powerfully head home a Bellamy corner.
Michu had been signalling throughout the passage of play that he was carrying an injury, and skipper Williams appeared to let the bench know in no uncertain terms a replacement should have been readied as his side effectively played with a passenger.
Caulker then made a telling contribution at the other end, bravely getting in to prevent substitute Wilfried Bony, on for the injured Michu, tapping in an equaliser from De Guzman's header back across goal.
But the goal had clearly stunned Swansea, and their confidence seemed to evaporate as a hungry Cardiff tore at them, with Vorm twice saving from substitute Campbell.
Swansea's misery was completed when Vorm saw red after racing from his area and clattering into Campbell, leaving Dean with little choice.
With all of their substitutes used, Swansea had to throw Rangel into the goal for what time remained but Cardiff were unable to add to their tally.