England's Croft, who only returned from a broken neck in January, won his place in the side on the back of a dynamic performance against the New South Wales Waratahs last weekend and is expected to be a major threat in the line-out.
The loss of Davies would be more of a concern as he was switched to inside centre because of an injury to compatriot Jamie Roberts and there are no more fit specialist centres in the squad.
Defensive coach Farrell said the players had been rested after a particularly hard day on Thursday.
"It's a funny old week with the game on Tuesday so we decided to have a double day yesterday, a really intense, physical session," he said.
"Tom's just got a little inflammation in his toe, nothing to worry about whatsoever. The important thing is he trained yesterday and got through the two sessions and the right thing to do is to give him a rest today.
"Jonathan Davies didn't train neither, because of the two sessions, just stiffness, that's all. Owen (Farrell) ran in there so it's fine."
Farrell said winger George North, an injury doubt with a hamstring problem earlier in the week, had shown no reaction to the injury and was expected to be available to play the full 80 minutes at Lang Park on Saturday.
Injury-prone Wallabies number eight Wycliff Palu also failed to take to the training pitch on a wet day in Brisbane with captain James Horwell saying he had "split himself", or cut his head, in an intense training session on Thursday.