Auimatagi won a majority judges' decision after 10 competitive rounds to take Jackson's NZPBA Middleweight and UBF Asia Pacific Middleweight titles.
It was Jackson's last fight at the weight before he drops down to Super Welterweight where trainer Chris Walker has high hopes for his technically excellent fighter.
Walker admits a late change in opponent upset Jackson's preparation and played a part in his defeat.
"On paper the opponent Gunnar fought is an opponent he should have beaten to be quite fair," Walker said.
"What probably made a little bit of an impact was the opponent change. We had been set to fight Jordan Tai, which was going to be a real challenging fight and Gunnar was quite amped for that.
"So it was actually quite hard for Gunnar to get up for [Friday's] fight and during the fight it was actually hard to get him motivated and get him into second and third gear.
"But that is boxing and you have to deal with those sorts of things but unfortunately we didn't deal with it that well.
"He is capable of putting in a better performance than that. He has proved that in the past.
"His timing was a little bit out, nothing was really flowing and he couldn't get that intensity going to put some pressure on the young boy.
"We knew it wasn't an easy fight. He is no mug."
Combat sport expert and ringside commentator on Friday night Mike Angove says Jackson didn't control the pace of the fight.
"Auimatagi is coming down from a slightly heavier weight and that certainly had some effect on Gunnar," Angove said.
"He is also young, hungry and very strong and he didn't allow Gunnar to come in and apply his usual pressure game with full confidence.
"He allowed Auimatagi to lead off early and dictate the pace particularly through the middle rounds, which made it very difficult for Gunnar to come back in those final rounds ...
"Auimatagi probably won more clear rounds and some of those other rounds were very, very close. That made it difficult and left it in the hands of the judges."
Jackson won plenty of plaudits for the classy way he dealt with the decision live on television.
"[You] gotta give credit when credit is due," Jackson said.
"A well-deserved win from the young fighter.
"This loss has made me hungrier for my next outing."
Jackson is back in the ring on August 13 when he challenges for the NZ Super Welterweight title in Auckland.
