However nine minutes after the restart and England were level thanks to Chris Robshaw's score and then ahead moments later after Farrell got in on the act and converted.
And Mowen, who made his debut for Australia in the first Test of the British & Irish Lions series and went on to feature in all three, believes they missed a trick after returning from the interval.
"It's hugely disappointing," said Mowen, who replaced the Australia captain of the British & Irish Lions series James Horwill as skipper for the England clash.
"Just after half-time was a real opportunity for us to skip ahead and put pressure on England, but we missed a few of those opportunities and they were extremely urgent and beat us on a couple of retreats.
"When you have that urgency, married up with a few things going your way, they created that momentum and took those two tries, so you've got to give them that respect."