PNGHS beat New Plymouth Girls' High in the other morning match to set up the final.
Watkin then scored 79 out of WHS's total of 118-6, with McGuinness the next highest contributor on 17.
However, the Manawatu school reached 119-6 midway through the final over.
"It was exciting ... if you're on the other side," said WHS coach Andrew Lock.
"That's the closest we've ever come for nationals, it doesn't come much closer than two balls."
The games finished an extraordinary school cricket year for Watkin, who scored 618 runs in girls matches.
She also scored a century in a T20 match for the WHS First XI, which added to her innings for the Central Districts Hinds and in senior men's club cricket for St Johns Tech meant she would have likely scored over 1000 runs for the season.