Smith tweaked a hamstring at training on Thursday and wasn't risked, leaving him to sit on the sideline at Forsyth Barr Stadium and watch his team nab a bonus point win against the winless Rebels.
Smith's injury isn't serious - he could return to play the Blues at home next Saturday night - and meant Matt Faddes started at fullback and Tei Walden shuffled into the match-day 23.
Up 20-0 with only 25 minutes on the clock against a lethargic and error riddled outfit from Melbourne, the game was as good as over.
At times the visitors looked so disinterested you had to wonder if somebody had slipped them a bunch of sleeping tablets pre-match.
As if the Highlanders, who were expertly captained by Luke Whitelock with Smith out, needed extra help.
They were already jacked up in a bid to mark halfback Aaron Smith's 100th match with a win, and made their intentions clear with a couple of monster scrums in the early stages.
Centre Malakai Fekitoa crossed for the opener in the 13th minute, when he collected a sharp offload from Richard Buckman and steamrolled Rebels winger Tom English on his way to the line.
As good as Buckman's pass was, it was the Highlanders' forwards who deserved the biggest pat on the back, given they shunted the Rebels off the ball at scrum time to create the opportunity.
Match Stats — Team Stats
Whitelock was the beneficiary of a lovely Tom Franklin off-load to score under the sticks less than five minutes later, finishing a 10-plus phase movement.
Gareth Evans, Buckman, Greg Pleasants-Tate and Fekitoa, who nabbed a late 40m intercept try, scored the other tries in the romp.
"It was good to score those tries and put away one of the weakest teams in the competition," Highlanders coach Tony Brown said.
"We didn't quite get the rub of the green in our first two games at home, so it's great to win this game at home and get a bonus point try.
"We've got a massive challenge next week against the Blues. I'd say they're going to be at least three times as good as the Rebels."
Buckman scored courtesy of a quick tap, the conclusion to a patch of play which, given the string of handling errors from both sides, some might wonder if the stadium roof had been leaking.
At times, the mistakes were comical.
Within a couple of minutes late in the first half, Rebels James Hanson and Jordy Reid, who had a game to forget, collected the ball inside their own 22, only to clumsily step on the touch line.
Such a rabble were the Rebels, the Otago Boys' High School First XV probably could have trotted out at halftime and finished the job off.
But the Highlanders were far from perfect themselves.
Sure, they crossed for six tries, but they also wasted plenty of other opportunities. Their clean out work at the breakdown left plenty to be desired, while protection for Smith was also lacking.
Wingers Patrick Osborne and Tevita Li were both guilty of over-doing the chip and chase - a puzzling option given the Highlanders were crossing the advantage line with ease for much of the game.
Marty Banks, starting for the first time this season, had a fine game with the boot, nailing all eight of his shots at goal.
English and Reece Hodge ran in slick tries for the visitors in the second half, but ultimately they were no match for the Highlanders.
Australian Super Rugby sides have now won just three of the last 33 games against Kiwi teams.
With the bonus point win, the Highlanders have 14 points in the bag and at least temporarily surpassed the Blues in the New Zealand conference.
The Blues have a chance to leap past them when they host the Force in Auckland on Saturday night.
Brown is hopeful Smith will be available for the game, but admitted there was no guarantee with hamstring injuries, which have also sidelined Lima Sopoaga and Waisake Naholo.
"Hamstrings are a funny one, so we just need to see how he wakes up tomorrow and progresses over the next few days."
Highlanders 51 (Malakai Fekitoa 2, Luke Whitelock, Richard Buckman, Gareth Evans tries; Marty Banks 3 pen, 5 con, Fletcher Smith con) Melbourne Rebels 12 (Tom English, Reece Hodge; Hodge con). HT: 20-0
Photo: JOE ALLISON (Highlanders centre Malakai Fekitoa attempts to offload against the Rebels in Dunedin on Friday night).