Fraser backed the 17-year-old as they weathered the early storm, holding off strike bowlers Carter Andrews and Zack Benton – who both took four wickets on day one – while working the singles and twos.
In the perfect finish, Fraser reached his sixth century for Wanganui, again tied with Central Districts Stags batsman Ben Smith for the association record, before smacking the required six runs for the win, his second six to go with eight boundaries.
"It's a pretty happy camp," Wanganui coach Warren Marr said.
"Yesterday [Saturday] was two poor batting sides – the ball swung and everyone's come off Twenty20s – it was just the one partnership that got away from us.
"Today, conditions were easier.
"If we got, to be honest, the [key] partnership [we'd win]. With the old dog and the young pup – that's amazing.
"A great feeling – Shaun has a big future in cricket. He's just so coachable.
"We timed it to perfection. It was just a great run chase."
In a good bowling effort on Saturday, paceman John Beale got key wickets on the top and then cleaned up the lower order for an impressive 6-34 from his 12.4 overs.
"I've never been involved when there's been three [new entries] on the Honours Board in one game," Marr said.
In his first game as captain, Chris Sharrock took seven catches behind the stumps across both innings.
Scoreboard
Horowhenua-Kāpiti 1st innings
D Sanson ct C Hobbs b J Beale 13
A Kumar ct C Sharrock b J Beale 0
A Simpson ct M Fraser b C O'Leary 0
B Tomo ct C Sharrock b S O'Leary 38
D Reder ct F Kinnerley b L Woolston 78
K Maclachlan b L Woolston 17
J Pinfold ct C Sharrock b J Beale 9
C Andrews ct C Sharrock b J Beale 0
X Sakhalkar lbw b J Beale 2
D Kennett not out 0
T Harris ct H Morrison b J Beale 0
Extras: 4
Total: 161(49.4 overs).
Bowling: C O'Leary 14 overs, 0 maidens, 43 runs, 1 wicket; John Beale 12.4-2-34-6; Hunter Morrison 4-1-27-0; F Kinnerley 5-1-19-0; Shaun O'Leary 8-3-15-1; Levi Woolston 6-0-23-2.
Wanganui 1st innings
A Penn ct J Pinfold b C Andrews 3
C Stewart ct J Pinfold b C Andrews 15
M Fraser ct J Pinfold b C Andrews 13
S O'Leary ct D Sanson b D Kennett 4
C Hobbs b Z Benton 7
C Sharrock ct J Pinfold b X Sakhalkar 3
J McIlraith b Z Benton 17
L Woolston b C Andrews 1
F Kinnerley lbw b Z Benton 8
J Beale ct D Reder b Z Benton 7
C O'Leary not out 6
Extras: 8
Total: 92 (37.1 overs).
Bowling: C Andrews 12-2-32-4; D Kennett 8-2-21-1; X Sakhalkar 7-5-4-1; Z Benton 9.1-3-26-4; T Harris 1-0-2-0-0.
Horowhenua-Kāpiti 2nd innings
D Sanson ct C Sharrock b F Kinnerley 77
A Kumar ct C Sharrock b C O'Leary 23
D Kennett ct C Sharrock b S O'Leary 10
A Simpson b L Woolston 12
B Te Tomo not out 48
D Reder c S O'Leary b L Woolston 16
K Maclachlan lbw b J Beale 12
Extras: 6
Total: 204-6 declared (57.2 overs)
Bowling: C O'Leary 12-2-33-1; J Beale 12.2-0-60-1; S O'Leary 16-2-48-1; L Woolston 10- 0-42-2; Fraser Kinnerley 7-2-19-1.
Wanganui 2nd innings
C Stewart lbw b Z Benton 21
A Penn lbw b X Sakhalkar 17
L Woolston b X Sakhalkar 4
S O'Leary not out 121
M Fraser not out 106
Extras: 6
Total: 275-3 (70.2 overs)
Bowling: C Andrews 13.2-4-46-0; D Kennett 13-1-50-0; X Sakhalkar 11-2-43-2; Z Benton15-2-50-1; Thomas Harris 10-4-37-0; Keegan Maclachlan 5-1-19-0; D Reder 3-0-26-0.
Result: Wanganui win by seven wickets, Horowhenua-Kāpiti take 1st innings points
