Erik Pieters was penalised for bringing down Samuel Eto'o just outside the penalty area in the 28th minute of the fourth round clash, and Oscar sent the resulting set-piece curling into the top left-hand corner.
Chelsea hit the post twice thereafter, but Hughes believes the goal was a pivotal point in the match.
"Obviously it was a fantastic strike, but I didn't feel it was a free-kick," he told ITV.
Despite Stoke's inability to fight back from being a goal down, Hughes insists there are positives to be drawn from the encounter.
"We couldn't quite create enough clear openings," he continued. "They are very adept on the break, so it was difficult for us, but I'm pleased with what we did.
"We stuck at it and didn't go under, made sure we were resolute, blocked shots when we had to, had good defensive awareness and tried to go the other way as well.
"We're disappointed to go out of the cup obviously, but there were more positives than negatives I would suggest."
Chlesea's reward for their win is a fifth round tie with Manchester City.
