Wellington are now looking like prime contenders to be relegated from the Premiership and it's a long way back from here if they want to make the playoffs.
After both sides exchanged penalties in the second spell, Manawatu first-five Otere Black finished off a sweeping breakout for the visitors as he scored next to the posts.
After adding the extras, Manawatu held a seven-point advantage as the game edged towards the final quarter.
With 20 minutes left, reserve halfback Jamie Booth celebrated his Manawatu debut in perfect fashion with a try that eventually helped secure victory, despite a late Wellington surge.
Black's accurate boot also proved decisive as he finished with 22 points.
Manawatu, who will host Bay of Plenty next Wednesday, have now won two from three and will fancy their chances of pushing towards the playoffs in the Championship.
Wellington will travel to Eden Park to meet Auckland next Saturday as they look to resurrect their ailing campaign, which is bordering on a disaster.
Manawatu 27 (Otere Black, Jamie Booth tries; Black 5 pen, con) Wellington 21 (Jason Woodward, Tolu Fahamokioa tries; 3 pen, con) halftime: 6-6