Watson developed a calf strain and will miss the Sydney Test, while Clarke also remains in doubt.
Melbourne: Australia's second Test thrashing of an injury-ravaged Sri Lanka provided some consolation after a stinging 1-0 loss in the home series to South Africa, but has left the team with much to ponder ahead of the dead rubber Test in Sydney next week.
Australia head into the final match of the series with an unassailable 2-0 lead, but the innings victory in Melbourne was soured with ongoing injury clouds over skipper Michael Clarke and vice-captain Shane Watson.
The fitness concerns have added further ammunition to critics of the team's player management, with selectors and fitness staff already under fire for a controversial rotation policy that saw injury-free seamer Mitchell Starc rested for Melbourne for fear he might break down.
Both Watson and Clarke played despite bringing injuries into the Melbourne Test, leaving selectors open to accusations of double standards. While Clarke scored a glittering 106 and Watson a solid 83 to help set up victory, the wash-out from Melbourne will do little to quell the grumbling.
Allrounder Watson broke down with a calf strain after bowling on day one and will miss the Sydney Test, while Clarke remains in doubt as he continues his battle to recover from a hamstring strain.
When asked why selectors had not rested the injury-prone Watson, who was forced to shoulder a big bowling workload in the first Test victory in Hobart when seamer Ben Hilfenhaus broke down with a side strain, Cricket Australia's high performance chief Pat Howard told reporters: "There was some consideration of it."
"But it was looked at as a collective. He's multi-skilled and can bring more than a couple of attributes to the game.
"When we talk about players missing a game or managing their workload, a lot of this is around young fast bowlers and looking after them is a pretty core principle of what we're trying to do."
The support staff's best intentions have not stopped young pacemen James Pattinson and Pat Cummins from breaking down among a raft of injuries, while 22-year-old Starc's Melbourne omission left the bowler tweeting that he was "shattered" by the decision.
Selectors have also backed themselves into a corner by promising Starc would play at the Sydney Cricket Ground, meaning either one of Mitchell Johnson, Peter Siddle or Jackson Bird must miss out on a wicket traditionally conducive to spin.
Man-of-the-match Johnson, had a brilliant return to form in Melbourne after being dumped for the Hobart Test, capturing six wickets and bashing an unbeaten 92 in a performance that would virtually guarantee selection. Bird also had an excellent Test debut with four wickets in place of the injured Hilfenhaus, while pace attack leader Siddle might not take kindly to being left out after being controversially rested for Australia's third test loss to South Africa in Perth.
Cricket Australia can scarcely clutch at fatigue as an excuse in their selection deliberations, with the three quicks hardly breaking a sweat in the two and a half day Test in Melbourne. Watson's injury has opened the door for uncapped Glenn Maxwell, but re-opened a can of worms as to what to do with the barrel-chested vice captain.
Debate has long raged as to Watson's relative value as a batsman or bowler, and the risk of him being both. Watson, himself, said he was having doubts about carrying on in both roles.
"I am certainly doing some thinking about what my prospects are moving forward, with my bowling especially," Watson, who will have played only three of the six home Tests this summer, told Australia's Channel Nine.
Clarke, on Australia's five-man selection panel, emphatically backed Watson to continue as an allrounder after the Melbourne Test. But another injury could test Clarke's support, with the need for a settled lineup to tackle India on tour in February and March ahead of the first Ashes campaign in July.
"We want to keep getting better every day. And we aren't good enough to play players at 70 or 80 per cent," Clarke said.
"You need to be able to be at your best."