After a goalless opening period, the Potters took the lead four minutes after the re-start via a strike from on-loan Liverpool winger Oussama Assaidi.
But Everton pressed forward in search of an equaliser and forced the draw when Jermaine Pennant fouled fellow substitute Leon Osman in the box, with Leighton Baines duly dispatching the resulting spot kick in injury time.
The draw saw Stoke halt a two-match losing run after away defeats to Newcastle and Spurs, while also extending their unbeaten home record in the league to seven games.
Asked if he was frustrated after the draw, Hughes told Sky Sports: "Well, you get to that stage of the game when you think you've seen the game out.
"I thought we'd played really well today, great in every aspect really - (we were) on the front foot and bounced back certainly from a poor performance against Spurs.
"But today we were right on the money I felt and really restricted Everton to very few real clear-cut chances.
"I felt we were always in the game in terms of possession and chances created, certainly in the first half, I thought we were excellent.
"Towards the end of the second half, obviously we were 1-0 to the good and they started throwing people forward so we had to just dig in and try and protect what we had.
"Unfortunately we made a mistake and conceded a penalty and they were able to take something out of the game.
"But in terms of the game as a whole, I felt we deserved three points today."