The Dockers had named 21 of the 22 who played in the 2013 Grand Final for their final practice match at Patersons Stadium ahead of their round one opener with Collingwood on March 14.
However, Ballantyne was withdrawn from the squad on Wednesday after only doing some light running at training on Tuesday, with Tanner Smith replacing Ballantyne in the squad.
The Dockers have endured an indifferent pre-season to date having started their preparations later than most due to the Grand Final.
The Eagles hammered the Dockers by 84 points at Arena Joondalup in their first NAB Challenge encounter.
They recovered with a hard-fought 28-point win over the Western Bulldogs last week but defender Paul Duffield says the side is still searching for a more complete performance.
"We've talked about it in our review that the first half probably wasn't up to our standards against the Bulldogs," Duffield said.
"We certainly started to get to work in the second half and again that is something we hope to continue to build on and improve on and hopefully it's more of a four-quarter performance.
The 28-year-old signed a one-year contract extension last week that will see him remain at the club until the end of the 2015 season.
Duffield has played 133 matches across nine seasons after being elevated off the rookie list.
Despite being eligible for free agency at the end of this season, Duffield says his decision to sign a contract extension was an easy one.
"I love the club," Duffield said."I've very much enjoyed my time here. It's a great time to be at the football club. I'm really looking forward to the future."
Thursday’s practice match has been moved to 6pm AWST after both teams agreed to delay the start due to the heat.
