Clarke did not train at the Adelaide Oval today, a day after rolling his right ankle during fielding drills.
But the Australia camp says their skipper is a certain starter against England in the Test starting Thursday.
"It's more precautionary today," Watson said of Clarke’s absence. “Obviously Michael batted beautifully in the first Test as well, so his preparation was always going to be very good anyway.
"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."
Watson wants more bowling duties on a predicted flat Adelaide pitch in a bid to shield Australia's fast bowling ranks from burn-out with just a three-day turnaround for the third Test in Perth.
"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," Watson said.
"So there is no doubt I know that is a really important role (for me), especially with back-to-back Test matches as well, and how important it is for our quicks to be able to get through this Test match and bowl well, and also pull up well.
"Because Perth, we certainly know we have got the bowlers to be able to really exploit that Perth wicket as well."
Watson overcame a hamstring injury to play in Australia's series-opening triumph in Brisbane, but bowled just two overs as the tourists were skittled for 136 and 179.
"The bowlers certainly looked after me physically in the first Test, I wasn't really called on to bowl," he said.
"But I know this is my turn to put my hand up and bowl the overs to look after those guys."
Watson returned with his injury from Australia's limited overs tour of India, and had no longer form cricket leading into the first Test – a factor he blamed for his meagre batting returns of 22 and six in Brisbane.
"I'm certainly going to be in a better place now after just getting through that one game," he said.
"Unfortunately (I was) not being able to concentrate for a long enough period of time to be able to bat for what I need to in a Test match.
"Certainly it was unfortunate that I wasn't able to adapt my game quick enough with not playing any four-day cricket or domestic cricket in the lead-up."