Despite leading 14-11 at half time, the hosts were unable to see out the match as the Wallabies fought back to claim the victory.
"I'm disappointed we lost but I thought Australia played a smart game and bounced back from their defeat against France last week and were competitive in all areas," said Lancaster.
"There were lots of positives from our own performance but the reality is we needed to take the opportunities we created, especially in the last 20 minutes when we thought our tempo would pay.
"They are the lessons we have to learn for South Africa next week."
England host the Springboks at Twickenham next Saturday.