Boak was unable to train on Friday after pulling up sore from Thursday's session, while Matt White was also withdrawn having failed to recover from a foot injury.
By resting the pair this weekend, coach Ken Hinkley hoped they would be available for the club's crucial encounter with the Sydney Swans next week.
He said the side would be ably led in Boak's absence by vice-captain Ebert.
"Both [Boak and White] did some running yesterday, we thought they both may come up but as we got there this morning and got them going it was clear that they weren't going to be able to play," Hinkley said.
"We're very hopeful that it's only one [week they'll miss], that's why we have to make that call now and make sure we don't make them multiple weeks by playing them.
"It's the second opportunity Brad's had to lead the club since he and Trav have been in control…if Travis is our first choice, Brad's clearly our second choice to lead the club."
Sam Gray and Ben Newton will replace Boak and White in the named 22, while John Butcher and Cam O'Shea join Jake Neade as emergencies.
Hinkley downplayed the loss of his captain and the impressive Richmond recruit.
"You would like to think you play a style of football that's not personnel-based, it's more team based and hopefully we're able to show that again [on Saturday]," he said.
"We're reasonably comfortable with the output of the players who are coming in and we're really comfortable with the team – the way we structure up, the way we play.
"It's always about team defence and as long as that's ok, we’ll be alright."
Saturday will be the first time Hinkley has coached against his former director of coaching Alan Richardson for premiership points.
Richardson played an integral part in helping the Power surge into last year's semi-final against Geelong, after the club finished 14th on the ladder in 2012.
But Hinkley talked down the impact Richardson's 'inside knowledge' would have on game day.
"I know St Kilda players well even though I don't coach them – that's our jobs," he said.
"It’s who's on top and the 22 that are on the ground and that will be the biggest determining factor."
