Clarke, who has overcome an ankle injury, was struck by a rising delivery from fit-again paceman James Pattinson while batting in the WACA nets.
On Wednesday, David Warner fractured his left thumb after copping a blow from left-arm pace ace Mitchell Johnson.
But while Warner is almost certain to be ruled out of the series, Clarke recovered from the hit from Pattinson and will lead the team against the West Indies.
"I feel really good. My ankle's come along really well after spraining it in Hobart," said Clarke, who missed the final ODI against Sri Lanka.
"I'm at full fitness. I've been doing all my running. I've had plenty of batting since I've been here, some bowling and lots of fielding.
"I'm 100 per cent and looking forward to being out there."
Clarke said batsman Usman Khawaja, who was named as a replacement for Warner, would play in the first one-dayer against the West Indies, but there was no room for Ben Cutting and Xavier Doherty in the final XI.
Tasmanian James Faulkner will make his ODI debut.
Australia team: Michael Clarke (capt), George Bailey, Aaron Finch, Phillip Hughes, Mitchell Johnson, James Faulkner, Glenn Maxwell, Clint McKay, Mitchell Starc, Matthew Wade, Usman Khawaja.