A six-under-par 66 gave the Welshman, winner of the title two years ago and joint sixth last February after a closing 66, a one-stroke lead over Ryder Cup team-mate Jose Maria Olazabal.
Scotland's Andrew Coltart, England's Martin Gates and German Thomas Gogele all returned 68s to share third place with Australian Robert Allenby.
Ernie Els, who found it hard to lead from the front at last week's Johnnie Walker Classic and was beaten in a play-off by Tiger Woods, will this time have to come from behind. He opened with a 70.
Woosnam, five weeks away from his 40th birthday, missed the half-way cut in Phuket and flew straight to Perth troubled by a trapped nerve. After treatment he could still feel throbbing in his fingers, but you would never have guessed it from the way he played.
Despite having to contend with the 'Freemantle Doctor' wind, which picked up once Olazabal was safely in the clubhouse, 1991 Masters champion Woosnam did not drop a stroke.
He looked in danger of doing so at the 170-yard 13th after pushing his tee shot into sand - but promptly holed out from there for his fifth birdie of the day. Another came on the par five last and he said: "When you're playing well you don't notice the wind so much."