McDonald, Crystal Palace midfielder Nick 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 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 World Cup.
Belgian-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.
The 28-man squad is one more than originally flagged after Verbeek convinced Football Federation Australia to allow him 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 World Cup squad when it is announced on June 1.
The Socceroos will leave on Wednesday for Johannesburg.