Cricket legend Warne, who died of a heart attack on March 4 in Thailand, was a life-long St Kilda fan.
Saints players wore black armbands in Warne's honour during Friday night's game at Marvel Stadium.
They also donned shirts during the warm-up with "WARNE 23" on the back, instead of their usual numbers, and a video tribute to Warne will be played on the venue's new big screens at halftime.
The Saints had "#23" and "#708" painted on the Marvel Stadium turf, representing Warne's playing number and his total haul of Test match wickets.
"It's a sad moment," St Kilda coach Brett Ratten told Fox Footy before the match.
"Warnie ... what an icon, what a person. He was probably our greatest (cricket) player of all-time.
"The great thing tonight is we'll be honouring Shane.
"We've got 50,000 members and hopefully he's there watching and the chants go out for him."
Warne reached out to Ratten over summer to offer his support to the Saints' football department.
"He was talking about helping out with some of our leadership program and how he could help," Ratten said.
"I could just see the passion that he just wanted our club to be as best as they could be, and each of the individuals.
"That was the type of person that he was. He wasn't worried about his time, he just wanted to help.
"What a special man, it's very sad and our thoughts go out to his family, especially tonight."
Wearing a St Kilda scarf, 22-year-old Jackson embraced Saints captain Jack Steele at the coin toss and had two attempts at flipping it before it landed flat on the grass.
In a statement earlier this month, Jackson described his father as his "brother, my best friend".
Warne, who died aged 52, was a dedicated St Kilda supporter and played in the club's under-19s team.
He will be farewelled at a private family funeral on Sunday morning.
A state memorial will be held on March 30 at the MCG, where the Great Southern Stand will be renamed in Warne's honour.
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