The visitors couldn't capitalise further, and looked to have conceded when former All Black Malakai Fekitoa crashed over in the 18th minute.
Referee Shuhei Kubo ruled the Toulon-bound midfielder had lost the ball forward over the line, however, leaving Auckland scoreless.
They did manage to see out the rest of their spell with 14 men without conceding, Jono Hickey's 21st minute penalty levelling the scores just before Trainor's return.
Auckland looked good on the counter-attack, but continued to have trouble nailing the final pass in gusty winds and sweeping rain.
They finally delivered five minutes out from halftime, replacement hooker Kurt Eklund barging over from the confusion of a disorganised attacking line-out.
Hickey's conversion gave Auckland a 10-3 lead at the break, a margin they struggled to extend despite the improving conditions.
Northland struck back with a devastating counter-attack down the left touch after 53 minutes, good support play finished with a storming try to Crusaders wing Jone Macilai.
The try went unconverted, and with neither team managing any real territorial dominance, Auckland did enough to hold on for the win.