The Melbourne Rebels' slim hopes of making the Super Rugby Pacific finals have suffered a hammer blow after their clash with the Highlanders ended in heartbreaking fashion in Dunedin.

As the match looked headed towards golden point, Highlanders centre Sam Gilbert booted the winning penalty in the 84th minute to break the deadlock and seal a 20-17 victory.

Both teams went into Saturday's game on 15 points, three outside of the finals-bound top eight and desperate for victory.

Gilbert stepped up after Rebels No.8 Richard Hardwick, who had been one of their best, was pinged at the breakdown - one of a number of suspect calls by referee Paul Williams.

Highlanders winger Jona Nareki somehow avoided a penalty despite dragging a Rebels player by the foot after he was tackled, which contributed to a Melbourne knock-on as they hunted a match-winning try at the death.

While frustrated Melbourne coach Kevin Foote said his team didn't do themselves any favours with 17 turnovers, he was unhappy with the refereeing inconsistencies.

"I'm disappointed in some of those decisions," Foote told AAP.

"We're going to have to look hard at them but I think there's a lack of consistency across the board.

"There was a lot of off-the-ball stuff as well and we've got the fourth official (Television Match Official) and some of it's guessing and some of it's not even accurate."

Melbourne were forced to play the final 10 minutes with 14 men after Jordan Uelese was given a yellow card after the reserve hooker brought down a Highlanders player without the ball, mistiming his tackle.

It was a heavy price with Gilbert also booting a penalty to tie up the match at 17-17.

With in-form playmaker Carter Gordon missing the match with a bruised knee and Reece Hodge at five eighth for the first time this season, Melbourne's attack lacked punch and polish early on.

The Highlanders also made life difficult for the visitors at the breakdown by playing usual loose forwards All Black Shannon Frizell and Max Hicks in the second-row.

The home side looked to have crossed after two minutes but Rebels winger Lachie Anderson somehow got his hand under the ball to stop Gilbert grounding it.

Former Sevens star Anderson also pulled off a try-saving tackle later in the half when he bumped a surging Sean Withy into touch.

Fullback Andrew Kellaway also got in on the action when managed to roll and hold up Highlanders flanker James Lentjes over the line in the 75th minute.

The Highlanders did manage to score in the 13th minute through fullback Connor Garden-Bachop before Melbourne levelled when Hardwick dived across from the back of the ruck.

With turnovers cruelling the Rebels' attack, the Dunedin side went into halftime up 14-7 after All Blacks prop Ethan de Groot broke through.

Melbourne again locked up the game when centre Stacey Ili found a hole and then a Hodge penalty gave the team a 17-14 lead.

But it didn't prove enough to keep the home side at bay, with Melbourne's season now effectively over with two rounds to play.

"A lot was riding on it (the result) but every week has been like that ... we're just not finishing at the end," Foote said.

"It's going to depend on a couple of results unfortunately but I think we've played well this year, we just haven't got the results."