Clarke, his country's best batsman, rolled his right ankle in training on Monday but later batted in the nets without obvious signs of discomfort.
"Michael Clarke is not training today," a team spokesman said in Adelaide, where the second Test starts on Thursday.
"His ankle is a bit stiff, sore. He will train tomorrow and will play in the game."
Australia is used to pre-Test concerns over the fitness of Clarke, who has suffered from a degenerative back condition for several years.
Clarke scored a century as the hosts, aiming to prevent England from claiming a fourth successive Ashes series, won the opening Test by 381 runs in Brisbane to take a 1-0 lead in the five-match series.
All-rounder Watson, no stranger to injury problems himself, said the rest was "precautionary" and Clarke would not be hampered by one day fewer in the nets.
"Obviously Michael batted beautifully in the first Test so his preparation was always going to be very good anyway," he said.
"I know the medical staff and Michael are very confident. It was just giving him a break today and he'll be training flat-out tomorrow, ready to go for Thursday."
All-rounder Watson was Australia's main injury concern before the first Test and the hamstring injury he was battling in the days running up to the Gabba opener meant he bowled sparingly.
The 32-year-old is now fit and ready to lend a hand to the fast-bowling trio of Mitchell Johnson, Peter Siddle and Ryan Harris, who will have only a few days to rest after Adelaide before the third Test in Perth.
"The bowlers certainly looked after me physically in the first Test, I wasn't really called on to bowl," he added.
"But I know this is my turn to put my hand up and bowl the overs to look after those guys.
"The wicket is going to be flat, the bowlers are potentially going to have to bowl many more overs compared to Brisbane to be able to bowl the English out.
"And (it's) important for our quicks to be able to get through this Test match and bowl well and also pull up well because we certainly know we have got the bowlers to be able to really exploit that Perth wicket as well."
Despite Australia's thumping victory in Brisbane, Watson was disappointing with the bat and managed to contribute only 28 runs over two innings.
"I'm certainly going to be in a better place now after just getting through that one game," he said.
"Unfortunately (I was) not able to concentrate for a long enough period of time to be able to bat for what I need to in a Test match."