Magpies forward Ginnivan was caught high by Mason Redman during the first quarter of Sunday's thrilling win over Essendon but did not receive a whistle in his favour.
It came just days after the league moved to clarify its high contact rule, following fierce debate around whether Ginnivan was being umpired differently to other players.
The league had said players would not be given free kicks when they ducked or shrugged in tackles to create high contact.
Ginnivan was cited as one of three examples in the league's memo and has been an unwitting lightning rod this season for criticism of players who attempt to draw free kicks.
Shaw said the umpires' treatment of Ginnivan had been "disgraceful".
"This issue won't go away even after a great game," the Magpies' 1990 premiership captain posted on Twitter.
"The AFL has persecuted a player on a whim and now has again opened up umpires to embarrassment due to this Ginnivan interpretation."
Collingwood president Jeff Browne said the club would take up the issue with the AFL umpiring department.
"We need to clarify this with the umpires, no question about that," Browne told 3AW.
"I don't know whether it's personal but it's obviously a directive and in that particular case it was incorrectly applied.
"We need to speak up about that."
Richmond legend Matthew Richardson said the Ginnivan-Redman non-call was "outrageous", while former Magpies hero Mick McGuane said whistleblowers should "umpire the rules of the game, not the player".
The AFL is yet to clarify whether it believes the decision was correct.
Collingwood ruck-forward Mason Cox also weighed in, questioning the league's commitment to player welfare around head contact.
"Wild to think high tackles were put in the game to protect players' health and now are being blatantly ignored for a 19-year-old," Cox posted on Twitter.
"How can we think 'the AFL cares about concussions and head high contact' after this."
Collingwood coach Craig McRae offered Ginnivan his support post-match.
"I thought that was a free kick. He just tackled him high," McRae said.
"I don't think there was any leaning into it.
"I'm clear with it (the rule). The umpires have come to our training.
"We won't make blame, or excuses around things. Umpires get some right, some wrong."
