He had to share the spoils with fellow apprentice Holly Durnan in the Play On, For Neale (1600m) when Kaleo and Dirnaseer could not be split before scoring on Duchess Zou in the 20 Years of Living Legends Trophy (1400m).
Both Johnstone winners were prepared by Maher.
"In racing, things happen, and you have to move on to the next thing in the space of race-to-race," Johnstone said after his dead-heat win aboard Kaleo.
"It was a bit of a messy start my first ride at Flemington with the saddle up on its ears, but I went out on this one confident and with a clear head.
"His last start was really good, and I knew the track would be no problem," Johnstone said.
"I knew if he got the first half of the race right, he would have that good turn of foot late, which we did."