Munster, who trailed 6-3 at half-time, struggled in the scrum and had front rowers Damien Varley and Wian du Preez sin-binned as the Italians put the pressure on and opened up a match-winning lead at 16-3.
Into the final quarter and with their replacements making an impact, Munster crossed for two tries from stand-in captain Doug Howlett and James Coughlan.
But crucially Paul Warwick could only convert one of them, and de Waal's 74th-minute penalty was left as the clinching score.
It was a significant win for Franco Smith's men - their first since the Christmas double over Aironi - and just reward for a heroic display from their forwards.
Flanker Padro was a forceful ball carrier, captain Enrico Pavanello led by example in the second row and the front row combination earned their corn with a strong display of scrummaging.
It was Munster's first defeat in 12 matches against Italian opposition and cuts their lead at the top of the table to seven points.
Injuries and international commitments robbed Munster of a big chunk of their senior squad, but head coach Tony McGahan was offering no excuses afterwards.
"I was just very annoyed with our performance. You can't come to a place like this and expect to win if you don't have any platform to play off," he said.
"I thought we were lethargic in the first half and obviously our set piece was in trouble for most of the game. They scrummaged really well, they were looking to draw penalties and we were unable to cope with that."
Out-half Paul Warwick converted the first of his two penalty attempts in the opening quarter-hour, and Munster seemed to settle well.
However, issues soon arose with their scrum and de Waal needed no second invitation to open Treviso's account. In only his third league appearance for the club, the South African slotted kicks after 17 and 28 minutes.
He made a great connection with a long range penalty to move Treviso ahead at 6-3, rewarding his forwards for exerting pressure at a scrum near the halfway line.
Before that, centre Andrea Pratichetti failed to hear James Jones' whistle as he darted through to score behind the posts. Full-back Brendan Williams joined the attack at pace, but a forward pass was spotted by the match officials before Pratichetti was released.
Seven minutes before the break, Munster showed what they could do in attack. A strong carry from number 8 Coughlan brought them into the Treviso 22 and scrum half Duncan Williams was hauled down just short of the whitewash.
At the ensuing ruck, Treviso's Franco Sbaraglini went in off his feet and killed Munster ball and referee Jones reached for his yellow card.
de Waal was narrowly wide with another monster penalty in the closing stages of the first half, and a concerted spell of possession amounted to nothing as Munster were quick to seal off the space.
The hunger and will to win was obvious from Treviso as they began the second half with real intent. Padro slipped through a tackle in midfield, only for a subsequent knock on to halt his side's advances.
Treviso then won a scrum against the head and after hooker Varley was sin-binned for infringing at a ruck, de Waal extended the hosts' lead to 9-3.
Munster stayed patient and retained possession through a series of phases in the Treviso half. Warwick, Coughlan and Howlett got more involved, but the frustation was obvious when a forward pass from Ian Nagle spoilt a promising position.
Then du Preez saw yellow for a scrum infringement as Treviso shunted the Munster forwards back. The game opened up on the hour mark, with Howlett covering 40 metres on a pacy counter attack. Replacement centre Sam Tuitupou also got on the ball.
The home side's greater urgency and accurate passing, with Tobie Botes to the fore in that regard, paved the way for Padro's try. A neat necklace of passes put him over in the right corner pasy Warwick and Scott Deasy.
A brilliant conversion was added by de Waal, who curled it just inside the left hand post, and it looked a long road back for Munster at 16-3 down.
They covered the first steps with a second penalty of the afternoon from Warwick. Then, with 67 minutes on the clock, Howlett's momentum took him over the try-line after the ball was swept right in a flowing move. Warwick's missed conversion left it at 16-11.
de Waal calmly kicked another meaty penalty to leave Treviso, who were cheered on by a passionate home crowd, on course for a famous win.
Fresh legs off the bench got Munster back probing for a try. Their efforts were rewarded when Coughlan got over after a succession of forward drives.
Warwick added the conversion this time, leaving just the minimum between the sides with time almost up. But the territory was with the Italians in the closing minutes and a final knock on from Munster just about summed up their day.
|Benetton Treviso Score Card|
|Willem de Waal||1||4||14|
|Munster Rugby Score Card|