Danny Welbeck opened the scoring for Albion in the 84th minute before Said Benrahma netted for the Hammers just three minutes later.
The result leaves a serious dent in the Hammers’ hopes of securing Champions League qualification this season, but manager David Moyes still found time to praise the Seagulls in his post-match press conference.
He said: "I thought we played very well for long periods in the game, especially in the first-half.
"I felt Brighton improved in the second-half.
"We didn't do enough in the final third. Our decision making was poor and there was not enough quality in the pass.
"We gave away a really bad goal. We can't keep giving the opposition a goal.
"We've had games where we've gone three or four up and tonight could have been another one if we had clinical finishing.
"All credit to Brighton. I think they are a good side."
Next up for Brighton is a clash against newly-crowned champions Manchester City at the Amex Stadium.
For the first time in months, Albion will be able to welcome a limited number of supporters back to the ground after the government eased Coronavirus restrictions on Monday.
The Seagulls were beaten 1-0 when the two sides last played each other in the league, with Phil Foden bagging the vital goal.
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He said: "I thought we played very well for long periods in the game, especially in the first-half.