Lipinski had a scan on Friday afternoon after dislocating his left shoulder during the final term of the club's practice match against Hawthorn in Launceston last week.
He underwent surgery on Monday.
While no firm timeline has been placed on the midfielder's return to play, it is expected Lipinski will be available for selection following the mid-season bye period.
"We are disappointed for Pat who has undergone his second shoulder surgery in six months," Collingwood football manager Graham Wright said in a statement.
"The expectation is that he will be out of the selection frame until the after the mid-season bye."
Lipinski played 25 games for the Magpies last season after crossing from the Bulldogs at the end of 2021.
The 24-year-old averaged a career-high 22 disposals and three clearances to help propel the Magpies to the preliminary finals.
Meanwhile, star North Melbourne forward Cam Zurhaar could miss the round-one clash with West Coast after suffering a calf injury.
Zurhaar strained his left calf during last week's 58-point loss to the Western Bulldogs and now faces a race against time to be fit for the March 18 match against West Coast at Marvel Stadium.
"Cam will be on light duties and monitored closely over the next week," Kangaroos football manager Todd Viney said in a statement.
"It will be a matter of waiting to see how he responds, then progressing his rehab as his symptoms allow."
The Kangaroos were dealt another blow when ruckman Callum Coleman-Jones suffered a partial tear of his left plantar fascia during Saturday's VFL win over Footscray.
The former Tiger will remain in a moon boot for a short period and will be progressed through a rehab program to allow his plantar fascia to heal.
West Coast have even bigger injury concerns - especially in the ruck department.
Nic Naitanui appears set to miss the start of the season due to ongoing soreness in his Achilles tendon.
Back-up ruckman Bailey Williams is also no guarantee to play after being forced out of last week's pre-season loss to Adelaide with a hamstring niggle.
Defender Josh Rotham, who was used as a second ruckman against the Crows, will miss at least a month of action after breaking his arm.
It means 22-year-old Callum Jamieson might be forced to lead the ruck against veteran Kangaroo Todd Goldstein.
Jamieson's back-up could be defender Harry Edwards or forward Jake Waterman, assuming West Coast want to keep Oscar Allen as a permanent forward.
Eagles forward Jack Darling is still nursing an ankle injury and is in some doubt for the club's season opener.
At the Western Bulldogs, livewire forward Cody Weightman still needs to overcome an adductor strain and Jason Johannisen is yet to fully recover from a calf issue.
Both face a battle to be cleared to take on Melbourne in round one.
But Taylor Duryea (neck), Ed Richards (corked quad) and Hayden Crozier (dislocated finger) are set to be available despite failing to finish the practice match against North Melbourne because of injuries.
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