Defender Jules Kounde put Sevilla in front in the first half after a stunning individual run while Ivan Rakitic added the second late on, after Barca had been denied a penalty and Lionel Messi had been thwarted three times by keeper Bono.
"It's a very tough punishment. We should have got a better result, we had a lot of chances and played well but leave here with a bad result," Koeman told a news conference.
"It did not reflect what we saw on the pitch."
The Dutchman also felt his side should have been awarded a penalty when Jordi Alba was fouled on the edge of the area and the referee awarded a free kick without reviewing the play with the video assistant referee.
The defeat ended a six-game winning streak for Barca in all competitions but Koeman said he was not worried the result would knock his side off course.
"I don't think this will affect us, we'll continue with the same mentality and commitment," he said.
"We've played 11 matches away from home this season and I would sign up to having the same results again. Of course I'd have preferred to have lost one more of those games and won today, but overall I cannot criticise the team."
He also believes his side are capable of turning the tie around in the second leg, just as they came from behind to beat Rayo Vallecano and Granada in the previous two rounds, adding: "When we're at home, Barca are capable of anything."
Sevilla coach Julen Lopetegui praised his side's performance but stressed the job was only half done.
"It was a beautiful victory against an extraordinary team and now we have to do the hardest thing of all, play in Barcelona. We know how difficult the return leg will be," he said.
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