Jozy Altidore put Sunderland ahead at the Stadium of Light before an unlikely brace from former Barcelona academy graduate Muniesa turned the game around.
Potters boss Hughes was surprised with the identity of his match winner, but was pleased that Muniesa could showcase what he was capable of, having not had many opportunities to do so.
Hughes told reporters: "Apparently he's only scored about three goals in his whole career, so he has nearly matched it.
"Given his pedigree, we know he's a technically-gifted football player and it doesn't matter where I play him - I have played him centre-half, I have played him left-back, he has probably got the ability to play in midfield as well, but he hasn't had those opportunities.
"But because of his technical ability when he finds himself in different areas of the field, he is able to make the right decisions and affect the game, which is what happened with his goals."
Muniesa, 22, has made just seven Premier League starts since moving to the Britannia Stadium on a free in 2013.