Blake Govers scored a hat-trick for the hosts, including a last-minute winner from a penalty corner.
Two Ashley Jackson goals put Britain 2-0 ahead, but Govers scored twice and Matthew Dawson once to put Australia in front, before Sam Ward made it 3-3.
Saturday's opening match ended 2-2, so the hosts hold a 1-0 series lead going into Tuesday's final Test in Perth.
It was the second time in two days that GB had squandered a winning position against the world's number-one ranked team.
"Our performance today was littered with inconsistency," said GB head coach Bobby Crutchley.
"We had some decent spells, but suffered too many turnovers in possession. We will be looking for improvement in the third Test."
Great Britain surrendered a two-goal lead to lose 4-3 to Australia in a dramatic second Test in Narrogin.