The Warriors looked set to share the spoils after tries by Harrison Hansen, Cameron Phelps and Amos Richards.
But wing Lupton stepped off the bench to score twice in either half, including the 75th winner.
It clinched only the second victory of the season for the struggling Crusaders.
Jason Van Dijk opened the scoring with a try the Crusaders deserved for their early pressure. The Crusaders skipper collected a scoring pass from Mark Bryant on 17 minutes.
But all the Welsh side's good work was undone when indecision in defence allowed Wigan's Hansen to pounce to level the scores.
But five minutes before half-time the Crusaders scored a thrilling breakaway try when Van Dyjk's clever kick put Peter Lupton through and they were ahead 12-6 at the break.
The Crusaders extended their lead on 54 minutes when a blistering run by Jason Chan was finished by Mark Dalle Court.
But late Wigan tries from Phelps and Richards brought the Warriors level once again before Lupton struck again five minutes from time.
SCORERS - Crusaders: tries Van Dijk, Lupton (2), Dalle Court; goals Lennon (3). Wigan: tries Hansen, Phelps, Roberts; goals Richards (2).
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