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The South African-born left-armer went into the semifinal as the competition's second leading wicket-taker with 20 wickets at an average of 18.10.
But he now occupies top spot after ripping through the Canterbury top order with three for 11 from seven overs.
It took just three deliveries to claim his first victim.
Pinch-hitter Iain Robertson dragged a delivery on to his stumps after trying to force it through the off side.
Wagner's old Transvaal teammate and Canterbury skipper Kruger van Wyk attempted to throw the bowler off his rhythm and walked down the track to a short delivery, succeeding only in nicking a pull shot through to the keeper.
Former New Zealand opener Michael Papps was the next to go when he was trapped in front by a quick, full delivery.
At 14 for three, Canterbury's innings was in ruins and the home side was never able to claw its way back into the match, thanks to a disciplined bowling performance from the visitors.
As well as Otago bowled, Canterbury will be ruing a woeful performance in which it was dismissed for a pitiful 86 on a flat but slow pitch at the Village Green.
Shane Bond sent some tremors through the Otago camp and gave a small crowd of about 500 something to cheer about when he removed opener Shaun Haig with his trademark inswinging yorker and bowled left-hander Greg Todd the next ball.
But captain Craig Cumming safely saw off the hat-trick ball and, together with Aaron Redmond, put on 77 for the third wicket as Otago cantered to victory with 36 overs and eight wickets remaining.
"This is what you play for," Wagner said.
"For us to make it to the final in my first season is just great and a massive privilege. Hopefully we take this form through and win the final."There were no demons in the wicket, Wagner said.
"It was pretty flat and slow and I just think we bowled really well."
Dimitri Mascarenhas bowled in tandem with Wagner and kept it tight from his end. The classy all-rounder bowled 10 overs on the trot and finished with figures of one for 16.
Warren McSkimming replaced Wagner at the crease and kept the pressure on.
He picked up his 100th one-day wicket when he nicked Ryan Burson out and took three for 13 from his eight overs.
Off-spinner Nathan McCullum was not letting up and claimed two for 23 from nine.
"We didn't allow them to play and from a coach's point of view, that is all you can ask of your team," Otago coach Mike Hesson said.
"When they did score boundaries they had to take risks and that is a sign of a well-disciplined performance.
"We were clinical and once we picked up a couple [of wickets] early, they went into their shell."Northern Districts has had the better of Otago this summer, winning both one-day matches.
Northern beat Otago by nine wickets in Alexandra in December but the sides had a much tighter encounter at Cobham Oval in Whangarei.
That game went down to the last over, with Northern winning by three wickets.
Otago, though, has the experience, having played in the last two finals. It is the defending champion and, in Cumming and Wagner, has two of the best players in the competition.
Wagner is the best bowler and Cumming is in fantastic form, timing the ball as well as at any time in his career.
M Papps lbw Wagner 5
I Robertson b Wagner 0
K van Wyk c de Boorder b Wagner 8
J Myburgh c de Boorder b McSkimming 4
S Stewart b Mascarenhas 5
C Anderson c Todd b McCullum 23
C Harris not out 12
A Ellis b Butler 8
S Bond c Cumming b McCullum 7
R Burson c de Boorder b McSkimming 4
L Burtt b McSkimming 0
Extras (5lb, 5w) 10
Total (39 overs) 86
Fall: 1/0, 2/13, 3/14, 4/24, 5/31, 6/57, 7/68, 8/79, 9.86.
Bowling: N Wagner 7 overs, 3 maidens, 11 runs, 3 wickets (2w); D Mascarenhas 10-1-16-1; W McSkimming 8-2-13-3 (2w); N McCullum 9-1-23-2; I Butler 5-0-18-1 (1w).
A Redmond not out 48
S Haig b S Bond 3
G Todd b S Bond 0
C Cumming not out 38
Extras (1wd) 1Total (2 wkts, 14 overs) 90
Fall: 1/5, 2/13.
Bowling: S Bond 5-0-39-2 (1w); L Burtt 2-0-9-0; R Burson 2-0-12-0; C Harris 2-0-11-0; A Ellis 3-1-19-0.
Result: Win to Otago by eight wickets.