The 24-year-old has been in terrific form in recent weeks, including scoring in Stoke's 3-2 victory over Arsenal last weekend.
And the forward once more looked lively as he had a huge hand in Peter Crouch's 13th-minute equaliser at Selhurst Park, after James McArthur had put the hosts ahead in Saturday's encounter.
However, Bojan was withdrawn in the second half with a blow to the hip and, although the injury is not thought to be serious, manager Hughes felt Stoke struggled to create chances after that.
"We probably missed the spark of Bojan in the second half where we had to make the change because of an injury," he said.
"He got a bang on the fleshy part just above the hip. I've had the injury before myself in the past and it's really painful.
"He'll be fine, he'll only be out a couple of days. When it happens it tightens up and restricts you immediately, he couldn't continue unfortunately.
"I think we probably missed that spark of his intelligence between the lines which he showed glimpses of in the first half, certainly when he was instrumental in our equaliser.
"So maybe that's why we weren't able to create as much in the second half."
Hughes also admitted doubts over Stoke's ability to complete a permanent deal for on-loan Chelsea winger Victor Moses - currently out of action with a thigh injury.
"If we had a significant amount of money [we would sign him] which I haven't," he added.
"I'd like to, he's a great kid. I saw him today, he's progressing well, he's got about three weeks I reckon before he's back."
