Ronan O'Gara kicked all of Munster's points at Musgrave Park as the Irish side secured their first win in three RaboDirect Pro12 games.
The returning Ireland fly-half fired over three penalties while a penalty from Aironi debutant Luciano Orquera made it 9-3 at the break.
Aironi's hopes of a comeback were hit when prop Fabio Staibano was sin-binned for dropping a scrum.
O'Gara brought his penalty tally to six before Orquera's late penalty.
Australian recruit Will Chambers got his hands on the ball before O'Gara sent over a well-judged penalty from the left for the fourth-minute opener.
Munster had a stranglehold on possession early on, O'Gara rewarding the home scrum with a second successful penalty.
But Orquera, who had missed an earlier effort from inside his own half, slotted a close-range 13th-minute penalty and Aironi soon made inroads into Munster territory.
They drew a penalty at the breakdown from an over-eager James Coughlan, but Orquera screwed his attempt wide from a very kickable position.
Damien Varley burst through the middle of a ruck to give the hosts some momentum, but he failed to find his man at the resulting lineout and Sinoti countered for the Italians.
Munster had to defend a couple of mauls before a back-handed pass from Chambers almost set up Johne Murphy for the game's first try-scoring chance.
Munster's attacks were too predictable at times and Aironi kept their discipline until Staibano was penalised at a scrum and O'Gara, into a fresh wind, pushed the lead out to six points.
Orquera missed an injury-time chance to reply, again from inside his own half, and O'Gara strengthened Munster's hand with two more three-pointers after the restart.
Paul O'Connell and his forward colleagues forced the issue coming to the hour mark, their scrum driving Aironi back, and the Italians' indiscipline was beginning to hurt them.
O'Gara followed his only miss with an accurate 57th-minute kick and Staibano was sin-binned soon after.
But Aironi dug deep while down to 14 men and even managed to add to their tally through Orquera's second penalty goal.
In a scrappy climax, Tomas O'Leary was forced off with a knock and Scott Deasy, already on for O'Gara, stepped in to play scrum-half.
Deasy was unfortunate when the ball fell off the kicking tee as he ran up to attempt a penalty.
The young half-back kicked two further penalties into touch, but Munster's experienced pack were unable to unlock Aironi's stubborn defence.
Munster: J Murphy; D Howlett, W Chambers, D Barnes, K Earls; R O'Gara, C Murray; W du Preez, D Varley, BJ Botha; D Ryan, P O'Connell capt ; D Leamy, P O'Mahony, J Coughlan.
Replacements: M Horan for du Preez (69), N Ronan for O'Mahony (34). Not Used: D Fogarty, J Hayes, D O'Callaghan, T O'Leary, S Deasy, L Mafi.
Aironi: R Trevisan; S Sinoti, A Masi, G Pavan, G Venditti; L Orquera, T Keats; J Sole, S Favaro, N Cattina; M Bortolami (capt), J Furno; F Staibano, F Ongaro, M Aguero.
Replacements: N Olivier for Orquera (74), S Perugini for Aguero (58), L Redolfini for Staibano (71), Q Geldenhuys for Furno (34). Not Used: R Santamaria, F Ferrarini, T Tebaldi, G Toniolatti.
Referee: Peter Allen (RFU)