Faddes darted over from close range and laid on a perfect ball for Jona Nareki as the two sides traded tries early on, with Auckland initially having the answers for Otago's early threat as they took a 19-17 lead into the break.
However, despite Auckland looking solid on attack, Faddes was too hot to handle for their defence, burrowing over from close range once more before completing his hat-trick. The 26-year-old showed excellent awareness, getting on the end of a kick which bounced between three Auckland defenders before spinning past that despairing trio and going over near the posts to give the visitors a 31-19 lead.
Auckland, who had looked unconvincing in barely holding off Taranaki the week before, struck back through Akira Ioane with 10 minutes to go, and while Otago nearly butchered their victory by conceding a penalty with six seconds to go, Auckland's final raid came to nothing, and they may now may struggle to keep their spot at the top of the table.
While they still lead the Premiership by three points, Auckland missed a glorious chance to build a handy buffer, and have a big showdown with Wellington looming on Thursday.
However, Otago have some significant prizes to play for now too – and if they keep playing like this, they just might win them.
Otago 31 (Matt Faddes 3, Vilimoni Koroi, Jona Nareki tries; Josh Ioane 3 cons)
Auckland 26 (Caleb Clarke, Dalton Papali'i, Tumua Manu, Akira Ioane tries; Harry Plummer 3 cons)
HT: 19-17