Coming into Tuesday night's clash at AAMI Park outside the top six and with just four games remaining in their seasons, both sides desperately needed three points.
Thanks to Andreas Kuen and Andrew Nabbout's goals, it was City who secured them.
"You don't have to be Einstein to realise the situation we're in and what we needed to do," said City boss Aurelio Vidmar.
Leapfrogging Macarthur into the sixth and final playoff spot, City will now host fellow finals aspirants Wellington on Sunday, with their destiny in their own hands.
But for the Mariners, who had surpassed all expectations by even being in finals contention rather than battling to avoid a wooden spoon, their finals hopes have been dealt a mortal blow.
Though Warren Moon kept the faith post-game, his side now sits in ninth spot, four points behind City.
And after playing Brisbane on Friday, they will end their season against the league's top two, Auckland and Newcastle.
"We've got three matches left; we'll go for three wins," said Moon.
"That'll take us to 37 points, and that means Macarthur, City and Wellington have to get 38.
"That's got to be our mindset."
City soon took control on Tuesday, and Kuen made the all-important breakthrough after dribbling to the top of the box and, with the aid of a wicked deflection, beating Andrew Redmayne.
The defending champions dominated in the following exchanges, with Daniel Arzani twice coming close to netting, but, as has repeatedly happened this campaign, they couldn't turn this purple patch into a two-goal buffer.
"Some of the football we played in that first half was the best we played most of the year," said Vidmar.
"We probably made it more difficult for ourselves.
"We should have been at least two, if not three, goals up at halftime for the amount of really good chances we had."
However, while Ali Auglah netted a 94th-minute consolation for the visitors, this didn't ultimately cost the hosts, who managed an early second-half push from the Mariners before securing a deserved cushion when Arzani teed up Nabbout for the winner.
"Daniel is certainly coming into his own now," said Vidmar.
"And his last couple of games, he's really starting to shine."
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