Meanwhile, the Brumbies sit in fourth and will host a playoff match, even though they sit 11 points behind the Crusaders.
It's the new Super Rugby structure that has quickly became a farce, and after this weekend, when the New Zealand teams outscored their opposition 237-71, it shows something needs to change.
New Zealand Rugby Union (NZRU) chief executive Steve Tew told Tony Veitch on Newstalk ZB that the playoff format, from a rugby point of view, just didn't feel right.
"It's not as complicated as it sounds, but frankly, it's just not fair."
Some argue that the Lions have proved their worth out of South Africa by topping the standings with a round to go, but there is a simple explanation for that.
The Sharks, Jaguares and Kings, all of whom belong to the same conference as the Lions, have just 13 combined wins in a total of 42 games. An easy conference to win games in, and an easy conference to top.
But when you have prominent players including Dane Coles, Cory Jane, Andy Ellis and Damian McKenzie, all speaking out about the confusion around the format, that has to be an indicator.
Jane told Tony Veitch that until last weekend, he wasn't even aware teams had to be seven points clear after scoring four tries to earn a bonus point.
Crusaders coach Todd Blackadder also said it was confusing for his players, and he was one of the first to stand up and raise concerns when the new format was announced.
He too doesn't think the format rewards the best teams.
"It just doesn't seem fair," Blackadder said. "Even the Stormers, they haven't had to face a New Zealand team and it looks like they will be hosting a quarterfinal."
"Hopefully common sense will prevail and we'll get a competition that rewards performance unlike this current model."
And across the ditch, Australian coach Michael Cheika agrees despite his local sides losing all four games against New Zealand teams this weekend.
"Until Super Rugby has a format where everyone plays everyone, you're always going to have these questions," Cheika said.
Super Rugby has just one more round left before the playoffs, and if the quarterfinals play out as plans, we could still see three New Zealand teams in the semifinals.