City had lost three games on the bounce and sat seventh heading into Saturday's match at AAMI Park.
But Wong's ripping strike in the 37th minute, his first professional goal, means Aurelio Vidmar's charges will finish the weekend inside the top six.
It delivers a crucial confidence boost ahead of next Saturday's derby with Melbourne Victory.
Wong is the club's youngest ALM goalscorer at 17 years, 132 days.
He was the first player to graduate to a full professional contract with City after starting with the club's school programs, and joined their academy as an 11-year-old in 2019.
Attacker Marco Tilio made his first start since November but with Samuel Souprayen and Kai Trewin unavailable, Aziz Behich was a makeshift centre-back next to German Ferreyra, with Callum Talbot at left-back
City were lively early and in the seventh minute, Steven Ugarkovic blasted over the bar.
Seven minutes later, Perth striker Patrick Wood required treatment after a cut to the face from a high boot from Ferreyra, but was able to play on.
Teammate Lachie Wales forced a fantastic diving save from Patrick Beach in the 16th minute, while Tomi Mrcela lashed a shot over the bar in the 22nd.
City's youth then started to make their mark.
Wong shot straight at Oli Sail in the 28th minute and Kavian Rahmani forced a save from the Perth goalkeeper a minute later.
City broke through when Tilio had a shot blocked and was then dispossessed, only for the ball to fall to Wong to blast an unstoppable strike into the top corner.
Minutes later, City had the ball in the back of the net after a dazzling Wong run but Max Caputo was offside when he tapped home.
Perth's William Freney blasted over late in the half.
The second half proved a relatively dour affair, but Ugarkovic was substituted with an apparent injury just after the hour mark.
Perth (10 points), sit 12th ahead of next Saturday's home clash with Sydney FC.
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