Coughlan crossed in the first half and Ronan O’Gara kicked the rest of the points but it was to prove a nail-biting and bad-tempered evening in the Welsh capital.
O’Gara suffered an off-day in front of goal, missing four kicks and 12 potentially crucial points that would have eased Munster nerves in the closing moments.
A feisty match saw three players shown yellow cards for punching but it was Munster who were left standing at the last bell to claim an important win.
The victory was their first away to Cardiff since November 2005 and ended their run of five defeats in Wales, in all competitions, but more importantly extended their lead in the Magners League to 13 points.
They also did Ulster a huge favour given that Cardiff, despite a losing bonus point, missed the chance to leapfrog them into the play-off places.
It was a job well done by Munster who welcomed both youth and experience to the team with the return of many of their brigade of Ireland stars, including captain Paul O’Connell and O’Gara, who helped guide young scrum-half Conor Murray through his biggest test yet.
However O’Gara failed to get the start he was looking for himself, pushing his first effort at goal wide just moments after Halfpenny opened the scoring for Cardiff.
That was in stark contrast to Felix Jones, who revelled in the open spaces afforded him by the Blues midfield. The 23-year-old full-back was showing great maturity as he picked his angles of running with expertise.
It was from his opportunism that the try was to eventually emanate, hacking ahead to have Cardiff scrambling back in defence. From there Denis Leamy went close before Keith Earls showed why he so dangerous in broken play.
The wing darted through a Blues defence at sixes and sevens and even when hauled down, had the presence of mind to find number eight Coughlan on his shoulder in support.
O’Gara converted only for Halfpenny to immediately claw back three points before a niggly contest soon erupted into a full-blooded brawl.
Wales prop John Yapp allowed his frustration at being held off the ball by Mick O’Driscoll to erupt and was sin binned for a wild swing.
O’Gara swept home two more penalties, either side of a fumble by Niall Ronan with the line at his mercy, following another break by Jones.
Still, 13-6 ahead was a comfortable position to be in after 25 minutes away from home, until the game exploded into life with eight minutes of the half remaining. An innocuous ruck inside Munster territory turned into a five-man brawl that saw Damien Varley and Sam Hobbs shown yellow cards.
Halfpenny slotted the resulting penalty and when Tony Buckley was reprimanded for needlessly infringing at a ruck, the Welshman slashed Munster’s lead to 13-12 at the break.
With Earls in electric form, Munster always looked dangerous and he stepped through two players and raced up field. Doug Howlett supported but failed to draw the last defender, Chris Czekaj, who was able to recover and bundle Murphy into touch.
O’Gara missed three times in the second half, though did managed to hit the target in the 59th minute after Dan Parks gave Cardiff the lead with a drop goal. That was to prove the final score as Munster’s defence held firm.
Scorers for Cardiff: L Halfpenny 4 pens; D Parks drp gl. Scorers for Munster: J Coughlan try; R O’Gara con, 3 pens.
CARDIFF BLUES: C Czekaj; R Mustoe, C Lualala, D Hewitt (J Roberts, 51), L Halfpenny; C Sweeney (D Parks, 51), L Williams (T Slater, 69); J Yapp (S Hobbs, 29), R Williams (K Dacey, 46, R Thomas, 65), S Andrews (N Trevett, 32-34), M Paterson, P Tito (capt, B Davies, 46), A Pretorious (S Hobbs, 23-29), X Rush (M Molitika, 60), M Williams.
MUNSTER: F Jones (S Tuitupou, 65); D Howlett, J Murphy, L Mafi, K Earls; R O’Gara, C Murray (P Stringer, 56); W du Preez (M Horan, 54), D Varley (M Sherry, 59), T Buckley (S Archer 11-18), M O’Driscoll (D Ryan, 59), P O’Connell (capt), D Leamy, J Coughlan, N Ronan (P O’Mahony, 59).
Referee: Alan Lewis (IRFU).