He had been scheduled to run in a barrier trial on Tuesday ahead of an autumn campaign .
"It's unfortunate Gr. 1 winning Samadoubt has picked up an injury. He has been fit, strong & ultra consistent for 5 seasons & unfortunately like any elite athlete, sometimes injuries happen. He'll head out for an extended break & return when 100%," Baker said on Twitter.
"The injury Samadoubt has suffered is a strained tendon. He will be treated intensively over the next few weeks followed by a long period of rest and rehabilitation. Tendon injuries are rare in our stable and it's dispiriting to have happened to such a wonderful horse."
Group One placegetter Champagne Cuddles was galloped on during the Magic Millions Snippets on Saturday and will head to the breeding barn next season.