Down 22-10 at the break, Wairarapa pressed their advantage as hooker Zac Wilkie scored early in the second half from a lineout, with Thompson landing his second consecutive sideline conversion by deflection off the right-hand post.
But just like the Heartland game, Wanganui were able to call on talented resources from the bench. Josaia Navitio came on as first-five and Grayson Tihema entered the game at fullback while taking over the goal kicking.
Granted a licence to run, both were outstanding as Wanganui suddenly woke up when the players remembered how to play their game.
Assisted by Wairarapa infringements, which led to yellow cards for second-five Pua Taffa and reserve forward Sam Barbour, Wanganui cut loose and suddenly the visitors could not force turnovers.
Navitio was hit hard from an offside player close to the line, but bounced straight up to take the tap and burrow over.
Second-five Mohi Waihi likewise slipped near the tryline, but recovered his feet and went himself, parting the defence to dive across.
Navitio made another midfield burst and beat two tacklers before finding reserve winger Jaye Flaws, who showed great upper-body strength to force the ball down under the posts.
Tied 29-29, Moli Sagapolutele all but scored from a scything 50m burst and Wairarapa were pinged at the breakdown, with Tihema raising the flags with eight minutes remaining.
The visitors desperately clawed their way back to Wanganui's line, but Tihema made a try-saving tackle in one corner and Hillis stole a lineout against the throw on the other to see the development team home.
But even here there were injury concerns for the wider Heartland squad as winger Aaron Vadiga went off from a head knock.