McDonald, Crystal Palace midfielder Nicky Carle and Norwegian-based defender Jade North were omitted when coach Pim Verbeek trimmed his provisional squad to 28 players ahead of this week's training camp in South Africa.
McDonald, 26, a prolific scorer for Celtic with 65 goals in 126 appearances before switching to Middlesbrough in the English Championship last season, yet again failed to find the net in Australia's 2-1 win over New Zealand in a FIFA World Cup warm-up game at the Melbourne Cricket Ground on Monday.
McDonald has now failed to score in 16 matches for his country and his omission leaves Verbeek with just three recognised strikers for the FIFA World Cup. Dutch-based Nikita Rukavytsya and Josh Kennedy of Nagoya Grampus will back up Harry Kewell in the striking department.
Verbeek admitted McDonald had struggled as the lone striker in his 4-5-1 playing system, and had missed out for that reason. "Scotty is a typical two-striker player and that's where he feels happy also," Verbeek told reporters.
"But we don't play with two strikers. We play with one striker up front and wingers, so Scotty doesn't fit in this system. He knows it, and he tried everything."
The 28-man squad is one more than originally flagged after Verbeek elected to take four goalkeepers into the South African training camp. Youngsters Tommy Oar and James Holland are still in the training squad, but Verbeek said they were effectively going for the experience and were unlikely to be part of the final 23-man FIFA World Cup squad when it is announced on 1 June.
Verbeek said the players from the provisional squad who did not make the final 23 would be kept on in South Africa for the duration of the tournament. The Socceroos will leave on Wednesday for Johannesburg.
They play friendlies against Denmark on 1 June and the United States on 5 June in Roodepoort ahead of their opening FIFA World Cup Group D match against Germany in Durban on 13 June.
Goalkeepers: Mark Schwarzer (Fulham/England), Adam Federici (Reading/England), Brad Jones (Middlesbrough/England), Eugene Galekovic (Adelaide United)
Defenders: Scott Chipperfield (Basel/Switzerland), David Carney (Twente/Netherlands), Lucas Neill (Galatasaray/Turkey), Michael Beauchamp (Al Jazira/United Arab Emirates), Shane Lowry (Aston Villa/England), Craig Moore (uncontracted), Mark Milligan (JEF United/Japan), Rhys Williams (Middlesbrough/England), Luke Wilkshire (Dinamo Moscow/Russia)
Midfielders: Mark Bresciano (Palermo/Italy), Tim Cahill (Everton/England), Jason Culina (Gold Coast United), Brett Emerton (Blackburn Rovers/England), Richard Garcia (Hull City/England), Vince Grella (Blackburn Rovers/England), James Holland (AZ Alkmaar/Netherlands), Brett Holman (AZ Alkmaar/Netherlands), Mile Jedinak (Antalyaspor/Turkey), Tommy Oar (Utrecht/Netherlands), Carl Valeri (Sassuolo/Italy), Dario Vidosic (Nuremberg/Germany)
Forwards: Josh Kennedy (Nagoya Grampus/Japan), Harry Kewell (Galatasaray/Turkey), Nikita Rukavytsya (Twente/Netherlands)
* Please note that squad lists only become official after they have been submitted to and announced by FIFA.