The Test No.5 has been ruled out of Australia's fifth and final ODI in Colombo on Friday with a hamstring injury.
It is understood Head ran more than 15 kms during game three, with the heavy grounds and humid conditions causing havoc with recovery.
The 28-year-old suffered the minor hamstring strain during the game four defeat but still managed to run more than 11kms.
Fast bowler Mitchell Starc (finger) and Steve Smith (quad) also remain on the sidelines for the dead-rubber match, after Sri Lanka wrapped up the series with their four-run win on Wednesday.
Having all three still on the sidelines is less than ideal preparation for the first Test in Galle, starting on Wednesday.
Australia's last Test series in Sri Lanka in 2016 ended in an embarrassing 3-0 whitewash.
"There's a lot of them," Australian white-ball captain Aaron Finch said when asked about the team's injuries.
"Travis Head will miss the next game with a hamstring injury.
"It's a bit more of a precaution, just where he fields he does a lot of kms out there and the ground is quite heavy.
"I'm not sure what he's looking like for the Test matches.
"Starc is still not right...the stitching and where it's at, it's just not quite 100 per cent healed so without being able to bowl with tape on, he'll be out."
Head enjoyed a breakout summer as he starred in Australia's Ashes demolition of England, scoring 357 runs at 59.5, including two centuries.
Josh Inglis could make his ODI debut as a replacement for Head, or Australia could opt to play an extra bowler for their last white-ball game of the tour.
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