The Magpies' 10.6 (66) to 6.5 (41) victory at Victoria Park was their highest-ever AFLW score and sent them six points clear of both the seventh-placed Bulldogs and eighth-placed Gold Coast.
But the win was soured when Bonnici had to be helped off the field in the first quarter after awkwardly landing from an aerial contest.
The 2021 All-Australian was consoled by sidelined captain Brianna Davey, who suffered a ruptured ACL earlier in the season.
Bonnici was later on crutches with her left knee iced.
"She's just being assessed, she'll go and have a scan but obviously it doesn't look good at this stage so we're expecting the worst," coach Steve Symonds said.
"The luck we've had so far this season along that track has got to indicate it's probably going to go the unfavourable way for us
"She's in great spirits and despite that, she's really proud of what the group was able to produce today and the group showed a bit of fight for her.
"We'll just get around her now and whatever the scan comes back and says, we'll just get around her and other players will have to step up."
Symonds said Bonnici had been crucial to keeping Collingwood's heads up in a period of mixed results, travel and tight turnarounds and her teammates had stepped up for her.
"Today we started to get closer to what we were," he said.
"We took the handbrake off a little bit and stopped playing it a little bit safe and just went for it a bit more."
Jaimee Lambert dominated, booting three goals from 22 disposals and was well-supported by Ruby Schleicher, Mikala Cann and Sarah Rowe.
Co-captain Steph Chiocci looked slick in her return from an achilles injury, while the recalled Sabrina Frederick booted 2.3 in her best game in black and white.
Bulldogs midfield gun Kirsty Lamb (21 disposals) booted the game's first goal and was influential around contests, along with Bulldogs skipper Ellie Blackburn (19 disposals, two goals).
The game was a see-sawing affair until the hard-running Magpies got on top in the second quarter, with three unanswered goals delivering a 17-point half-time lead.
The Magpies were down two players in the second half after losing Aliesha Newman to concussion, but Lambert nabbed three goals on the bounce in the third term to deliver an unassailable lead.
The Bulldogs bravely fought out their seventh game in 30 days but were unable to mount an unlikely comeback.
"It was a game plan we had in place that we wanted to play which was going to nullify them and play to our strengths," Bulldogs coach Nathan Burke said.
"We just weren't able to execute that for long enough and we paid the price, unfortunately."
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