Bopara opted for caution after he was left with the tail as England collapsed to defeat.
The 28-year-old hit 25 from 44 balls before he was controversially given out stumped by the television umpire following a freak dismissal.
Bopara's reticence to finish off the match has seen him criticised in some quarters, but Giles has sympathy for the player.
"It was a tricky situation," Giles told reporters. "A lot has been said about Ravi's cricket but I can only go on what he has played during my time as coach and he has been very good for the side.
"In the Champions Trophy he did well and okay at the end of our summer. He struggled on this tour with the bat and that can happen but he is a very useful cricketer.
"The situation he went in, we had just lost a couple of quick wickets. The two guys were in and suddenly he was put under the pump a bit. We know it was not easy on this wicket to start playing your shots. In the end he could have been a hero but it was one of the strangest dismissals I have ever seen in my life."
Bopara was given out after Australia wicketkeeper Matthew Wade spilled the ball onto the stumps.