Haley scorned the General Assembly vote as "political theater" and a waste of time.
Despite the US vote, the resolution condemning the ongoing economic embargo on Cuba passed overwhelmingly in the U.N. General Assembly, 191-2.
The move changed Washington's position after it chose to abstain from voting on the annual resolution last year under then-President Barack Obama, for the first time in 25 years.
The U.S. and Israel were the only dissenting voters in the 193-member General Assembly. The United States is traditionally isolated, with only Israel joining it in opposition.
The vote on the condemnation, which has become something of a ritual at the General Assembly, has taken place every year since the embargo was imposed. Haley explained that the about-face is because the election of Donald Trump as new president and herself as new United Nations ambassador.
USA officials say 21 embassy employees were deliberately targeted.
"I think this administration would regard that for far too long Cuba has engaged in human rights abuses - human rights abuses that perhaps past administrations have turned and looked the other way, and this administration continues to call upon Cuba to improve", State Department spokeswoman Heather Nauert said on Tuesday after announcing that Haley would vote against the resolution.
"The United States opposes this resolution today in continued solidarity with the Cuban people and in the hope that they will one day be free to choose their own destiny", she said. US investigators still do not know exactly who and what caused the injuries, but 15 Cuban diplomats were expelled from Washington in retaliation.
The vote comes as an ongoing crisis over US government workers in Havana harmed by invisible "health attacks" has created a new rift between the USA and Cuba, putting the restoration of ties in jeopardy. The U.S. embargo on Cuba is nearly universally opposed worldwide.
Cuba's foreign minister, Bruno Rodriguez Parrilla, dismissed Trump's charges, saying of the administration, "they lie when they talk of attacks or incidents".
The U.S. decision to stand by the more than five-decade-old embargo has always been condemned by other countries, including U.S. allies, and the Cuban government has long pinned economic woes in the country on the U.S. penalties.