Thomas Sorensen, Seyi Olofinjana and Dave Kitson were all handed home debuts by manager Tony Pulis - who also included midfielder Amdy Faye, on trial from Charlton, on the bench.
Defender Ryan Shawcross followed up his own header against the bar to put City ahead just before the half-hour, but former Birmingham striker Walter Pandiani equalised soon afterwards when he evaded several defenders to connect with Dier Sanjuto's cross.
The Potters were ahead again moments before the break when Shawcross' shot hit ex-Manchester United goalkeeper Ricardo and bounced into the net off the legs of Rory Delap.
Javad Nekounam ensured a share of the spoils for the Spaniards with a powerful header 15 minutes from time.
The result means Stoke - who kick off their first Premier League season against Bolton next weekend - have five wins, a draw and a defeat from their pre-season matches.