The Welshman saw his side break the deadlock through birthday boy Charlie Adam's penalty, but Theo Walcott levelled matters three minutes before the break.
Mesut Ozil struck only five minutes into the second half and substitute Alex Iwobi made it 3-1 and 15 consecutive home wins for Arsenal over Stoke in all competitions,
It was a result Hughes to rue the visitors' failure to reach the interval with their lead intact, who believed that Walcott's strike turned the tide.
"We stood up to them and maybe conceding the equaliser before half-time lifted them and hurt us more than we thought," he said.
"We created a number of good opportunities when in previous years we have struggled to even get shots on goal here. We had a number of good moments even before the penalty.
"We had to push the game and look for opportunities at the other end - a lot of teams will struggle to come here and cope with the pace and power Arsenal have at the moment.
"You have to take it on the chin and go again."
The spot-kick was awarded after Granit Xhaka clumsily elbowed Joe Allen in the area and, though Arsenal boss Arsene Wenger disagreed with referee Lee Mason's call, Hughes felt the official got it right.
He added: "I thought he [Allen] got sideswiped and was in possession of the ball in the box. My initial thought was it was a penalty."
Hughes left his news conference under a cloud after refusing to answer a question on his fans taunting Aaron Ramsey, who suffered a broken leg at Stoke in 2010.
Saturday's result was only the second loss Stoke have suffered in 10 games in all competitions and they remain 10th.