A controversial Robbie Brady penalty put Hull seventh in the Premier League as West Ham's problems continued.
The Irish winger slotted home after Joey O'Brien was judged to have shoved him, although contact appeared minimal.
Since winning their opening game against Cardiff, West Ham have picked up just two points from a possible 15. They have failed to score an away goal this season.
James Tomkins had a header cleared off the line and Razvan Rat fired over as the visitors pushed for an equaliser.
Hammers boss Sam Allardyce was further angered when his side, still without an away goal, were denied a late penalty for a handball.
Allardyce cut an animated figure on the touchline from the moment Brady went down under O'Brien's 11th-minute challenge after the ball had been lofted into the penalty area - and referee Kevin Friend stunned the Hammers by pointing to the spot.
The Tigers spent the rest of the game resolutely defending their lead to record their second straight win.
Big decisions went our way - Bruce
Steve Bruce's side have 10 points from their first six matches, but Hull fans have seen this before.
After promotion in 2008, they amassed 20 Premier League points by October before their form slumped.
But there is a sense that with Tom Huddlestone, Jake Livermore and Brady adding extra quality in midfield, the Tigers might now be better cut out for top-flight football.
Bruce wrote in his programme notes that he and Allardyce have been "mates for years", but there was little warmth in the West Ham manager's expression after Brady calmly scored Hull's opener.
The Hammers, who had previously managed only eight shots on target all season, rattled off several attempts in response but were wasteful in front of goal.
Their best effort came from Tomkins, but Ahmed Elmohamady was in the right place to clear off the line.
The Egyptian then went close himself in a rare Hull attack, but his powerful header was tipped around the post by West Ham goalkeeper Jussi Jaaskelainen.
Allardyce incensed by Brady 'dive'
The visitors continued to press after the break but found clear chances harder to come by - and Modibo Maiga toiled without reward up front in the absence of injured striker Andy Carroll.
The Tigers almost doubled their lead when Livermore fired against the post from the edge of the box - but the midfielder was then fortunate to see Friend wave away West Ham's appeals after he appeared to intercept a cross with his arm in the penalty area.
The visitors, who drew 0-0 in their two previous away games this season, chased an equaliser and full-back Rat struck an effort over the bar.
But for all their possession, the Hammers failed to seriously test Tigers goalkeeper Allan McGregor, and upcoming games against Tottenham and Manchester City could deepen their troubles.
Hull manager Steve Bruce:
"The big decisions have maybe gone our way but you can't mask that we created the better chances.
"I have seen the handball from Jake Livermore four or five times and can't see if it was deliberate or it hit him.
"From where the referee was standing and the linesman, they can't give it.
"I've not seen the penalty yet. We might have got the decisions but were still the better side on the day."
West Ham manager Sam Allardyce:
"The referee has given two really poor decisions.
"Brady takes a simulation on a slight contact with Joey O'Brien when the ball is not near him or the goal. He buys the penalty and the referee falls for it.
"Then Livermore puts his arm out and knocks the ball for a corner but the referee doesn't see it and doesn't give us a penalty.
"So it's our responsibility for not finishing our chances and the referee's as well for us losing the game."
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