Barker had Jimmy Spithill in trouble early on in the race, engineering a penalty on the US boat by preventing them from getting into the startbox on time.
The audacious move gave Team Japan a healthy lead off the line, which they managed to maintain over the first four legs.
But Spithill managed to set up a split in the fifth leg, sailing into better breeze than the Japanese boat to pull off the passing manoeuvre.
"Unfortunately we chose the wrong gate at the bottom and I can assure you it wasn't a deliberate act, if that's what you're asking," said Barker, when asked if was allowed to beat Oracle.
"It was disappointing to let that race slip away after getting out of phase at the bottom gate. It's part of racing. These boats are hard to manage in the light air, these are some of the hardest conditions to sail the boat in, and while it's frustrating there's still a long way to go in this competition."
Barker admitted he took some satisfaction over getting one over Spithill, his nemesis-turned-buddy, in the pre-start.
"It was quite pleasant pre-start, I certainly enjoyed the way that all kind of unfolded and the first two thirds of the race," he said.
Earlier in the day Team Japan claimed a crucial win over Groupama Team France, elevating themselves from the deadlock at the bottom of the table. The bottom-placed team after the round robin stage wraps up this weekend will be eliminated from the regatta.
"Every point is vital right now. We felt like we should have come away with a couple, but that's just the way it goes. That's yacht racing. We'll try and make sure we do a better job tomorrow [against Artemis]," said Barker.
