The Bosnia-Herzegovina international sat out Stoke City's 2-1 victory at West Brom on the final day of the Premier League season due to a stubbed toe.
Thomas Sorensen replaced Begovic for Sunday's clash at The Hawthorns, but Stoke manager Hughes is in no doubt that the 26-year-old will not miss out on a first World Cup appearance.
"I haven't asked too many questions about how it was done," Hughes told The Sentinel. "But I'm told the room was pitch black at the time.
"It was a nasty one because it raised the nail off the nail bed, but it is especially nasty for a goalkeeper.
"A keeper is looking for dynamic movements, whether he's diving or leaping, and so a bad toe injury like this can compromise him.
"It was quite obvious last Friday when he was trying to put his boot on that he was in difficulty.
"We thought about giving him a jab, but it then looked like he had got an infection and so there was no point.
"So he's now on a course of tablets and it was a shame he couldn't play the last game for us at West Brom, but the good news is he will be all right for the World Cup."
