Tries from Ross Ford, Ruaridh Jackson and Fraser Brown were not enough as Peceli Yato and Henry Seniloli crossed to add to 17 points from Ben Volavola.
After the match Gregor Townsend said: "Really disappointing we didn't win. The main parts of the game - the defence, the contact, our attack accuracy - weren't anywhere near where they need to be."
After a five-try win over Italy in Singapore and the victory against the Wallabies, hopes were high that Scotland would complete a clean sweep by putting Fiji away.
However, a team featuring 12 changes from the win in Sydney lacked cohesion in attack and struggled badly in defence, missing 30 tackles.
"For us to win Test matches we've got to defend really well - like we showed last week - and we probably missed too many tackles today," said Townsend, who tasted defeat for the first time as Scotland head coach.
"Fiji came alive when they broke those tackles. We've got to look after the ball, make sure we work teams in our attack and probably too many balls got dropped in contact with the wet ball."
Townsend, while acknowledging his own team's shortcomings, was keen to emphasise how well Fiji played, particularly a man the former Glasgow coach knows all too well - former Warriors lock Leone Nakarawa.
"Leone is an outstanding player, probably the best second-row in the world," said Townsend. "Certainly the best offloading player in the world.
"At times we defended him really well, we managed to close him down, but at other times he kept his energy, his line-break ability, and created a fantastic try.
"There were a number of Fijians that played really well. We didn't play as well as we have on tour, but I have to say credit to Fiji. They played some outstanding rugby, especially in that second half. They were tough to handle."
Despite the loss, Townsend says the experience will prove invaluable for the squad's future development.
"Hopefully we'll get more determination and realisation that if we don't do our defence well or get through our phases in attack then we're going to give teams opportunities to beat us," he added.
"We've got the template from last week on how we can beat the best teams in the world. This is a template to say 'this is how we're going to struggle against teams that are in the top 10, top 15 in the world, if we don't get things right'.
"It's not so good when you lose but there will be areas where we'll be a better team from what we've learned today."