Facer, a 16-year-old Otago Boys High School pupil, drove to the front of the green on the par-4 18th play-off hole, chipped short and two-putted for par.
Nicholson's drive finished on the 13th fairway, his recovery came up short and he made a bogey 5 when his par putt lipped out.
It was the first gross victory of note for Facer, who played well at the New Zealand Under-17 Championship on the North Shore course recently.
But it was Brandon Hodgson (Otago) who led the field at the halfway stage, just as he did during the 72-hole tournament at North Otago two weeks ago.
Hodgson started with a double-bogey 6 and turned 2 over after carding eight pars on the remaining front nine holes.
He made four birdies on the homeward nine for a 69 to lead by one from Facer at lunch.
Cameron Beel and Simon Gallie (both Otago) were two shots further back, while Brent McEwan (St Clair), the North Otago winner, was handy with 75 in the morning.
Hodgson fell away in the afternoon round with 79, while Facer carded a 3-over 74 to become the clubhouse leader.
McEwan had a sub-par 70 in the afternoon but came up one shot short of forcing a play-off with Facer.
Meanwhile, Nicholson was in one of the last groups to finish and he tied for the lead after 36 holes with his par round of 71.
