The match was won in the 11th minute when Jason Euell's cross was needlessly handled by Mark Kennedy and referee Kevin Wright pointed to the spot.
McGoldrick stepped up and placed the ball into the middle of the net, sending Dimi Konstantopoulos the wrong way.
Saints, playing the better football, came close again through Polish striker Marek Saganowski in the 25th minute.
Several passes were exchanged by the youthful home midfield, which led to a cross from Andrew Surman and Saganowski flung himself at the ball and saw his header flash wide.
Spurred on by the 2,000 travelling away fans, Cardiff almost levelled on the half-hour.
Captain Roger Johnson powerfully headed at goal but was denied by a reaction save from Kelvin Davis. In the following melee Scottish striker Ross McCormack looked certain to net, but Davis brilliantly scooped the ball away one-handed.
Following the double save, Davis sent Jason Euell on a quick break and he unleashed a shot which stung Konstantopoulos' hands.
Saints almost went two up before the break when danger-man Saganowski swivelled in the box and steered a curling shot inches wide.
The promotion hopefuls came close when McCormack fired a free-kick wide from 20 yards seconds after the restart.
The Welsh side pushed on and almost levelled in the 56th minute through Gabor Gyepes' header, after Gavin Rae's driven shot from the middle of the area was blocked.
This woke the home side up and on the hour they should have been given a second penalty, when Saganowski was tripped.
Sixty-five minutes in Saganowski was unlucky not to increase the lead after he hit the crossbar. A deep cross into the Cardiff area was volleyed at goal by the Polish striker and only a lick of paint saved the Welsh defence's blushes.
Cardiff penned the home side in for the last ten minutes and should have been awarded a penalty when the ball rolled down Chris Perry's arm.
The referee was unsighted and let play continue. The Cardiff players surrounded the official, but his decision had been made and Saints held on to a deserved three points.