England appeared in control early on day two at 65–1, leading by 99, before collapsing to 164 all out after losing four wickets for 11 runs in a post-lunch slide sparked by Scott Boland.
Set 205 to win, Australia needed just 28.2 overs as Head - promoted to open in place of the injured Usman Khawaja - struck a 69-ball hundred and finished with 123 from 83 deliveries.
Stokes said England tried several plans to halt Head but "he had an answer for absolutely everything," calling the innings "pretty phenomenal".
He rejected suggestions that England's aggressive batting approach was misguided, arguing that players who showed intent were the ones who found success on a bowler-friendly surface.
Despite the heavy defeat, Stokes highlighted England's first-innings bowling, which dismissed Australia for 132, as a key positive.
With a long break before the day-night Test in Brisbane on 4 December, he urged his side to absorb the disappointment but avoid carrying "baggage" into the second match.
"It's crucial we get back to the mindset we had before this game," Stokes said. "We need to win in Brisbane, and we're still confident in our abilities."
Stand-in captain Steve Smith struggled to contain his admiration after Travis Head's blistering 123 off 83 balls sealed Australia's two-day victory in the first Ashes Test in Perth.
All-rounder Senuran Muthusamy scored his maiden Test ton (109) and Marco Jansen smashed a brisk 93 (91) to boost South Africa to 480 all out on Day Two of the second Test.
Australia powered to an eight-wicket win against England in Perth, wrapping up the first Ashes Test inside two extraordinary days and moving 1-0 up in the five-match series.
Mitchell Starc took seven wickets but Ben Stokes replied with five of his own as England and Australia slugged out a 19-wicket opening day in the first Ashes Test in Perth.
