James Beattie's brace helped Stoke end a run of five Premier League games without a win while extending West Ham's winless run to seven games.
The striker smashed in a penalty after Matthew Etherington had been felled by Julien Faubert but Matthew Upson levelled with a free header.
Beattie tucked in Stoke's winner after Ricardo Fuller's angled shot had been pushed into his path by Robert Green.
Stoke's Robert Huth appeared to punch Upson late on but escaped punishment.
Referee Martin Atkinson and his fellow officials missed the incident despite the England centre-back being forced to leave the field with blood pouring from a wound near to his right eye.
Upson had been caught in the face by a stray Ryan Shawcross boot earlier in the game and Huth's flailing right arm, while the players were waiting for a West Ham free-kick to be delivered into the box, re-opened the wound.
Stoke ultimately deserved their victory for a typically tenacious and high-energy performance that unsettled the Hammers from the outset.
Pulis defends Stoke 'style'
Etherington, who played 195 times for West Ham, provided most of the early threat for the home side.
He raced on to Fuller's clever back-heeled pass before being scythed down by Faubert, who was booked for his challenge, to win the penalty.
Beattie's strike from the spot was clinical, flying beyond West Ham keeper Green's dive into his top right-hand corner.
Left winger Etherington then appeared on the right before cutting in on his favoured foot, but James Tomkins deflected his 25-yard effort wide.
West Ham, by contrast, were struggling to string passes together, although much of that was down to Tony Pulis's well-drilled Stoke side as to the failings of the Hammers to find their own players.
Alessandro Diamanti had their first shot on target some 30 minutes into the game, but even that came from a set-piece after he was fouled by Salif Diao.
The Italian picked himself up, but tamely struck the 30-yard free-kick straight at Thomas Sorensen in the Stoke goal.
But the Hammers were level a couple of minutes later when an uncharacteristic lapse of confidence in the home defence gifted them an equaliser.
It came from another set-piece as defender Upson was allowed to rise unchallenged eight yards out and powerfully nod in Mark Noble's corner.
After the break, West Ham boss Gianfranco Zola pushed Diamanti further forward to help top scorer Carlton Cole, who had spent the first half playing as a lone striker and being well marshalled by Stoke centre-back Shawcross.
Zola's decision almost paid dividends straight away as the midfielder produced a neat turn on the edge of the box, but his left-footed curling effort was comfortably saved by Sorensen, who later held a low striker from the Italian.
Stoke's forays forward were becoming increasingly rare, although Shawcross did momentarily leave his defending duties on Cole to head goalwards.
Shawcross' effort was blocked by Valon Behrami and he blazed the follow-up wide.
The centre-back was soon back on defensive alert though to block an effort from Cole, who had escaped his attention for the first and only time of the afternoon.
It proved a crucial intervention as moments later Beattie scored the winner.
Fuller skipped past Upson's challenge and raced into the box and when his angled low shot was pushed away by Green, the Stoke striker was on hand to turn the ball in from close range.
West Ham brought on striker Zavon Hines, but the youngster was unable to proved the spark West Ham needed.
And as the Hammers pushed more and more men forward in search of a second equaliser, Stoke were able to exploit the gaps opening up at the other end of the pitch.
And Etherington almost had the last word, but his header from Liam Lawrence's cross flew just wide.
