Bojan claimed the only goal at a rain-swept Goodison Park, converting a first-half penalty he had won himself when taking on James McCarthy.
The Spaniard has exhibited fine form in recent weeks and earned warm praise from his manager.
"Bojan did fantastic driving the game and carrying the ball and under those circumstances defenders know they have to be very careful. I thought it was a really good decision by the referee [to award a penalty]," said Hughes.
"If people see any weakness in Bojan's play they'll say he's not suited for the English game but in the short time he's been here I think he's knocked all those thoughts on the head.
"He is really enjoying his time here at the moment and what's happening to his football right now but he's worked really well and he'll see the rewards for that – and so will we."
Everton felt aggrieved when Jonathan Walters escaped a red card from referee Lee Mason, despite pulling down Leighton Baines when the full-back was through on goal.
Stoke broke from the resulting free-kick, and were awarded a penalty when Bojan was bundled over by McCarthy.
Although Everton applied pressure, Hughes felt his side were worthy winners.
"We had a gameplan and the key to it was to be nice and solid, and we were able to nip things in the bud and be on the front foot with our defending and then break from those positions," he added.
"I never felt Everton gained any real momentum in their play to ask any questions of us, and we saw the game out quite comfortably.
"Initially I thought the Jon Walters foul was just a coming together but having seen it again Jon does pull him back but Baines is quite far away so I think a yellow card was the right decision."
