Walatee struck in the fifth minute of Saturday night's match, but the visitors were forced to hold on for dear life in the second half as Perth launched wave after wave of attacks.
The home crowd became increasingly infuriated after Walatee went down several times for extended periods in what appeared to be an obvious intent to waste time.
Glory midfielder Nicholas Pennington became so frustrated at the extended time-wasting that he went over to Walatee and the group of Sydney players around him to vent his thoughts - leading to an angry shove.
Even referee Lachlan Keevers ended up losing his cool, handing Rhyan Grant and goalkeeper Harrison Devenish-Meares yellow cards for separate time-wasting incidents.
Glory came close to snaring the equaliser, but it wasn't to be, with Sydney almost snatching a second against the run of play when Patrick Wood launched a shot that forced Perth goalkeeper Matt Sutton into a sharp save in the dying moments.
Sydney's second win on the trot ensured they would again end the round on top of the table, boosting their tally to 18 points.
Glory, who entered the match aiming to post four wins in a row for the first time since 2021, are in fifth with 10 points.
Sydney coach Ufuk Talay defended 21-year-old Walatee, who was making his first start of the season and lasted until the 82nd minute.
"You've got to understand that it's his first start in a long time," Talay said of the former Western United attacker.
"He's come on for us, maybe a maximum of 30 minutes. So to push him that far, he was always going to cramp up, especially with the heat out there.
"He did a great job. He's an honest young player that if he's hurting, he's hurting."
Sydney were without star English midfielder Joe Lolley (hamstring), while Perth were missing last week's goalscorer Sebastian Despotovski (calf).
In an added blow for Glory, captain Adam Taggart limped off in the 40th minute with a groin injury.
Sydney came out of the blocks firing, with Al Hassan Toure's low cross finding its way to Walatee at the far post for an easy tap-in.
Glory didn't let the early blow affect their attacking intent.
Former Sky Blues striker Jaiden Kucharski almost scored twice against his former club.
His first shot deflected off a defender and bounced off the bar.
Kucharski put the ball in the back of the net in the 19th minute, but the referee deemed he had fouled his opponent just before the strike as he fought to win the bouncing ball.
Glory defender Brian Kaltak should have scored his fourth career goal in the 24th minute when he had a free header close to goal, but his weak glance meant it went wide of the target.
Taggart was also looking dangerous before being struck down by injury shortly before half-time, and Kucharski reluctantly came off with what looked like a hamstring concern in the 50th minute.
15°C