Aziz Behich's 17th-minute strike and a 76th-minute goal to Younis were enough to seal a third straight A-League Men win for City in a physical encounter on Sunday.
Younis almost scored one of the goals of the season in the 84th minute, only for his bicycle kick to be blocked on the line.
The result guaranteed City (35 points) will finish the round in sixth spot, just one point adrift of fifth-placed Melbourne Victory (36) and two behind both Adelaide and Sydney with two rounds remaining.
Phoenix (30) are now five points off sixth with just two games remaining.
"It's going to be tight," City coach Aurelio Vidmar told Paramount when asked about the battle for finals positions.
"It's been a crazy season all year, and it continues to be that, so who knows where it's going to finish."
There was plenty of frustration among City players in the first half.
Nathaniel Atkinson had to be calmed down by Samuel Souprayen in the 17th minute after unleashing a huge tirade on his teammate German Ferreyra for a defensive mistake.
And Elbasan Rashani yelled in frustration after teammate Andrew Nabbout got in the way of his shot.
But it was all smiles in the 27th minute when some fine lead-up play from Atkinson set up Behich, whose strike took a wicked deflection off Wellington defender Isaac Hughes.
There was physicality galore in the first half, with Phoenix striker Ifeanyi Eze left with a bloodied mouth after a swinging arm from Ferreyra.
The physicality kicked up a notch in the second half.
Eze shoved over Andreas Kuen just seconds after play resumed.
And in the 55th minute, the pair had to be separated after coming face-to-face following a tangle in the box involving numerous players.
There were more players suffering knocks than shots on goal by that point, but Younis came close to making it 2-0 in the 67th minute when he chested down a pass before whipping an attempt across the face of goal.
Younis finally nabbed the sealer in the 76th minute when he latched onto a beautiful slicing pass from Kuen and nailed a strike past the advancing goalkeeper.
Attacker Mathew Leckie, finally recovered from hip surgery, came on in the 83rd minute for his first ALM appearance since October 31.
"It was really good he was able to get on the pitch," Vidmar said.
"Hopefully he pulls up alright. He's been training the last two or three weeks with the group.Â
"He's feeling great some days, not the best other days, but this should give him a lot of confidence."
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