The Phoenix entered Friday's clash without star midfielder Michael McGlinchey, who flew back to New Zealand to be present for the birth of his daughter Annabel.
Glory made a dream start to the match when 17-year-old whiz kid De Silva scored after just 88 seconds.
Winger Youssouf Hersi set up the goal by cleverly skipping past Thomas Doyle and squaring a pass into the box, with De Silva chesting the bobbling ball home.
It was de Silva's second goal for the club after he also scored in the FFA Cup quarter-final win over Melbourne Victory.
The remainder of the half featured few clear-cut chances, with Hersi having a chuckle at himself after fluffing a running shot on goal in the 41st minute.
Keogh scored his fifth goal of the season when he stuck out his left boot to send Josh Risdon's pin-point cross into the back of the net.
But the Phoenix were back in the contest when Zadkovich's clumsy tackle on Lia earned him a red card.
Phoenix substitute Tyler Boyd earned his side a hat-trick when he clashed legs with Risdon, and Krishna made no mistake from the spot.
But Perth were able to hold on in the dying minutes to secure the win.
-AAP