Hill had 12 of his points on four straight 3-pointers as the Vandals (10-16) of the Western Athletic Conference took control of the game with a 16-5 run.
Idaho only had one basket over the final 5:27 but connected on 12 of 13 free throws.
The win was Idaho's first in Pocatello since 1996. The Vandals will rejoin the Big Sky Conference in 2014 for basketball and all sports but football, where they will be independent.
The game was part of the BracketBusters series, but the 101st between the schools.
Purdue coach Matt Painter says players haven't used the fifth-year graduate transfer rule for its true intent.
The dust has settled after players made their NBA draft decisions. Which college teams won? Which lost? Well, Villanova is pretty happy. USC, meanwhile, might not be as thrilled.
The 2017 recruiting class is short on point guards, with Trevon Duval leading only eight prospects from the ESPN 60 who are still available.