The 24-year-old went down in pain during the second quarter of the Magpies' victory over the Western Bulldogs at Victoria Park on Sunday.
"Unfortunately scans have confirmed what I had hoped so badly they would not," Bonnici wrote on Instagram.
"A torn ACL will see me sent to the sidelines for a while but every setback provides opportunity, I'm sure I'll find exactly that.
"Some hard work ahead but I'm ready for the challenge.
"Can't put into words how much the support means. Onwards and upwards from here."
Bonnici joins Magpies co-captain Brianna Davey on the sidelines after the joint reigning league best-and-fairest winner injured her knee in round one.
Collingwood's women's football boss Jess Burger said the Magpies were "hurting" for Bonnici.
"She is an incredibly strong leader of our club and this season she's taken her leadership to another level having been without Bri and at times Steph (Chiocci)," Burger said.
"She's continued to play some outstanding football this season and despite her injury, she should be extremely proud of what she has accomplished.
"Brit's professionalism and pride in preparation is second to none and I'm sure she'll continue these habits into her rehabilitation."
Bonnici will consult with her surgeon this week to plan out when to have her operation.
The list of AFLW players to have suffered ACL injuries this season has increased to eight with Bonnici joining the likes of Western Bulldogs ace Isabel Huntington and Brisbane Lions premiership hero Kate Lutkins among the unlucky collection.
St Kilda are, meanwhile, waiting on scans to Rhiannon Watt after the utility hurt her knee in the Saints' drought-breaking win against Gold Coast on Sunday.
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