"I haven't won anything in about 30 years, so I'm very happy."
Barltrop, who held a share of the overnight lead with England's Stuart Pond, birdied two of his first six holes over the Old Course to boost his title hopes.
He lost his momentum with a bogey at the ninth and a double bogey at the 10th.
A further bogey at the 15th cut his lead to one, but he rallied and managed to par the remaining three holes to fend off his rivals.
"I got off to a good start and established a decent lead but I almost gave it back to the rest of them around the turn," admitted Barltrop, a member at Royal Auckland Golf Club.
"But I played nicely after that and look forward to returning next year to try and defend my title."
Pethes was looking to become the first local player to win the championship since Terry Collins in 2004. He carded the best round of the day an even par 72.
Taranaki's Murray Martin finished in ninth place after carding an 83 in the final round.
Hong Kong Seniors Open Amateur Championship, Fanling -Results:
222 Michael Barltrop (NZ) 76 73 73
223 Joe Pethes (HK) 77 74 72, Rodney Barltrop (NZ) 76 74 73
225 Stefan Albinski (AUS) 78 74 73, Peter King (AUS) 76 75 74
228 Barry Downing (UK) 77 76 75, Stuart Pond (UK) 73 76 79
232 Kai Flint (GER) 80 74 78
233 Murray Martin (NZ) 75 75 83
234 Alex Ho (CH T) 76 78 80