Thistle held their two-goal lead until the last minute of the first half, when the home side scored from the penalty spot after a Thistle player was judged to have fouled a Whanganui forward in the penalty area.
Less than two minutes into the second half, Whanganui drew level with a far-post header from a left-wing corner.
The scores were level for 24 minutes and then, in the 71st minute, Whanganui scored with a 25-metre volley following a clearance from a left-wing corner.
The last four goals followed in quick succession . . . in the 74th, 77th, 78th and 83rd minutes.
Thistle went into the game having lost six players from the first-team squad for their previous home game, against Havelock North Wanderers on June 13.
Four players — Justo Rodriguez, Ema Martos, Agustin Ventre and Tomek Frooms — had gone to other clubs; Cullen Spawforth was serving a one-game suspension for accumulated cautions; and Kuba Jerabek was being rested because of injury.
At one stage on Saturday, Thistle had five teenagers on the field.
On Sunday at Childers Road Reserve, Thistle, who are now fifth in the nine-team league, play eighth-placed New Plymouth Rangers.