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Mauricio Pochettino's side had won all four matches at their new £1 billion Tottenham Hotspur stadium.
But Antonio's clinical second half strike ended that run as the West Ham winger became the first visiting player to score in the plush arena.
Third placed Tottenham's second defeat in their last three Premier League games put a dent in their bid to finish in the top four.
They hold a three-point lead over fourth placed Chelsea and are four points ahead of fifth placed Arsenal, with both team in action on Sunday.
It was a frustrating warm-up for Tottenham's Champions League semi-final first leg against Ajax in north London on Tuesday.
Pochettino had insisted Tottenham's first European semifinal since the 1984 UEFA Cup was less significant than their top four challenge.
But the Tottenham manager's team selection told a different story.
Tottenham defender Jan Vertonghen was absent with a reported injury as Pochettino made four changes, including resting Kieran Tripper, Victor Wanyama and Fernando Llorente.
Pochettino revealed this week that injured striker Harry Kane hopes to be fit for the Champions League final if Tottenham make it and the England captain was watching from the stands as his club's unbeaten start in the new stadium came to an end.
With Son Heung-min suspended for the Ajax first leg, Pochettino had no reason to rest the South Korea forward against the Hammers and he was swiftly into the action as he raced away for a shot that cleared the bar.
Son should have done better on that occasion and he fluffed his lines again with a low shot that was too close to Hammers keeper Lukasz Fabianski after Dele Alli's pass gave him a clear sight of goal.
West Ham finally broke out of their own half when Ryan Fredericks tested Hugo Lloris from long-range, but Tottenham remained on top as Lucas Moura drilled just wide of the far post.
A flowing Tottenham move unlocked the West Ham defence and Son's blocked effort dropped perfectly for Christian Eriksen, but the Dane smashed his close-range shot straight at Fabianski.
Tottenham found it tougher to maintain any momentum in the second half, with Son's unsuccessful penalty appeal, after being bundled over by Arthur Masuaku, made more in hope than expectation.
Manuel Pellegrini's team were growing in confidence and they ended Tottenham's unblemished record in their new arena in the 67th minute.
Marko Arnautovic chipped a superb pass towards Antonio and the winger controlled on his chest in the six-yard box before blasting a powerful finish past Lloris.
Celebrating with a bizarre bouncing motion, Antonio staged a joyous jig in front of the West Ham fans and he almost had them on their feet again in the closing minutes when his shot was pushed over by Lloris.
Tottenham looked tired in the closing stages, but they could have denied West Ham their first away win of 2019 when Vincent Janssen's stoppage-time header was cleared off the line by Fabian Balbuena.
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