The reigning champions passed Leicester's record of five wins on the road and are riding high at the top of Pool Four with three wins, thanks to victory at Leicester and now Cardiff.
In contrast, the Blues now face an uphill battle for Saturday's return-leg in Limerick having now twice been beaten at home in the cup.
A first-half try by No.8 Denis Leamy and O'Gara's faultless kicking saw Munster home as the guests ground out a win in the Arms Park mud.
British Lion O'Gara landed five penalties and a conversion for a 17-point personal haul that took him up to 803 Heineken Cup points - more than 150 ahead of his nearest rival.
The Blues made a bright start when Ben Blair landed two early penalties; the second resulting from Munster prop Fredericio Pucciariello punching as early as the 10th minute, and being shown the yellow card for his efforts.
However, Cardiff failed to make the numeric advantage count as Blair went wide with a penalty attempt before O'Gara landed his first kick to make it 6-3 after 20 minutes.
Martyn Williams was shown a yellow card for a high tackle as the Blues found themselves a man down and Munster made Cardiff pay with Pucciariello, back from the sin bin, brought down short of the line.
The Irish province grabbed their first try when Leamy was driven over the line by his pack and managed to touch down, despite landing on his back. O'Gara put the conversion straight between the posts and Munster were starting to turn the screw at 10-6.
Blues flanker Scott Morgan compounded his side's frustration after he barged O'Connell out of the line-out and O'Gara landed the resulting penalty on half-time to make it 13-6 at half-time.
The home side dug deep in the second-half as Blair landed two penalties to close the score to 13-12 going into the final quarter.
Yet O'Gara took over with three penalties in the last 20 minutes to see his side home, with Cardiff now facing the near-impossible task of winning at Thomond Park - where Munster have never lost a Heineken Cup match.
Cardiff Blues: Blair (4) pens
Munster: Leamy try, O'Gara con; O'Gara (5) pens