Midfielder Nick Carle and defender Jade North were the other two to miss out on a place in the 28-man squad following Monday's 2-1 victory over fellow World Cup finalists New Zealand.
Striker McDonald had enjoyed a prolific goal-scoring run in Scottish football with Motherwell and Celtic before moving to Middlesbrough in January, but he has failed to score for his country in 16 appearances.
Verbeek told reporters he did not feel McDonald could adapt to his prefered formation.
"Scotty is a typical two-striker player, and that's where he feels happy also," Verbeek said. "But we don't play with two strikers. We play with one striker up top and wingers, so Scotty doesn't fit in this system.
"He knows it, and he tried everything."
Injured Galatasaray forward Harry Kewell, Belgian-based Nikita Rukavytsya and Nagoya Grampus's Josh Kennedy are the only recognised strikers in the reduced squad.
The 28 players will fly to South Africa on Wednesday ahead of their last warm-up match against Denmark on June 1, when Verbeek will decide on his final 23-man squad.
Australia have been drawn in Group D for the June 11-July 11 finals with Germany, Serbia and Ghana.
Squad
Goalkeepers: Mark Schwarzer, Adam Federici, Brad Jones, Eugene Galekovic.
Defenders: Scott Chipperfield, David Carney, Lucas Neill, Michael Beauchamp, Shane Lowry, Craig Moore, Mark Milligan, Rhys Williams, Luke Wilkshire.
Midfielders: Vince Grella, Carl Valeri, Jason Culina, Mile Jedinak, Tim Cahill, Brett Holman, Dario Vidosic, Mark Bresciano, Brett Emerton, Richard Garcia, James Holland, Tommy Oar.
Strikers: Nikita Rukavytsya, Josh Kennedy, Harry Kewell.
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