The versatile player, not available for selection at his club, has pulled out of the squad ahead of the friendly against South American opposition this week
Herd was in contention to make his Socceroos debut but has now been replaced by Jeonbuk Motors defender Alex Wilkinson for Wednesday's friendly between Australia and Ecuador at The Den.
A statement from Villa read: "The club can confirm that due to personal reasons Chris Herd will be unavailable for selection until further notice. There will be no further comment and we request that Chris's privacy be respected."
Although the move from Villa looks like a blow to Herd's World Cup chances, Australian coach Ange Postecoglou said the 24-year-old uncapped Socceroo remained in contention.
"We have been made aware that Chris will be unavailable for selection at club level until further notice as he works through some personal issues and we will respect that and have replaced him in the squad for the Ecuador game," Postecoglou said in a statement.
"That presents another opportunity for Alex Wilkinson to come into the camp. He did well in the camp in Sydney last November when we played Costa Rica and he has a chance to put his best foot forward, like everyone else, in relation to World Cup selection."
Herd has only made two appearances for Villa this season, playing in losses to Fulham and Stoke last December.
However, despite recovering from a hamstring injury he has not featured in manager Paul Lambert's recent sides.