Clarke has been troubled by a hamstring injury since the First Test in Hobart and plugged on to play the Second Test in Melbourne last week, scoring a century.
Clarke was put through his paces by physio Alex Kountouris at the SCG on Tuesday, two days out from the Sydney Test, and seemed to have no problem completing the fitness session which included running and walking exercises.
Cowan was confident Clarke would lead the team into battle as Australia attempt to secure a clean-sweep of the series and send Mike Hussey into Test retirement a winner.
"I think everyone is assuming Michael's playing," said Cowan.
"He's certainly much better than he was two days out from the Melbourne Test and we saw what happened there so I think he's right to go mentally.
"Physically I imagine he'll get up for the Test match and we saw just another example of mind over matter or mind over body last Test when he batted so beautifully but didn't look inhibited in any way.
"It was a pretty inspirational innings I thought considering where he'd come from."
Cowan admitted there was a risk Australia could let their guard slip leading into a dead-rubber.
However, the left-hander says they were desperate to avoid complacency and had discussed that as a team.
"We have spoken at some length about our determination to make sure we win this series 3-0," he said.
"We've experienced some disappointment earlier in the season and this is us trying to vent that a little bit and we're pretty keen to see Mike off with flying colours.
"The end of a series sometimes training can become a little monotonous so it's important to try and stay sharp."