China, Russia, Saudi Arabia, Pakistan and Cuba, identified by the New York-based Human Rights Watch as unworthy of membership on the body, won seats along with 39 other countries.
But two others on the group's list, Iran and Azerbaijan, failed to win membership on the first ballot.
Human Rights Watch Executive Director Kenneth Roth said it was inevitable some rights foes would win seats but "the important step is that we have made real progress" over the discredited Human Rights Commission, shut down in March.
"It doesn't guarantee that the council will be a success, but it is a step in the right direction," Mr Roth said.
The United States, an outspoken critic of the old human rights commission, had decided against seeking a seat this year after voting against its creation, arguing barriers were too low to keep rights abusers from winning a seat.
US Ambassador John Bolton derided the inclusion of Cuba to the council and said it proved that Washington's concerns about the new panel were justified.
"What a joy," Mr Bolton said sarcastically of Havana's election. "That simply says that the deficiencies from the previous commission may well now still be carried over, as we sadly predicted when we voted against this resolution."
"Defeat" for US
Cuba, for its part, hailed its election to the Human Rights Council as a "resounding victory" for the communist regime and a "defeat" for the United States.
"The United States failed in its goal of preventing Cuba from getting a seat in the most important panel specialised in human rights in the United Nations," Cuba's foreign ministry said in Havana.
Elected on the first ballot were 13 African nations, 13 Asian states, three from Eastern Europe, eight from Latin America and the Caribbean and seven from the United Nations' Western Europe and other states regional bloc.
The council's architects had set a high bar for victory - attracting the votes of at least 96 UN members, an absolute majority of the General Assembly's 191 nations. Iran and Azerbaijan were among those falling short of that mark.
Another country that came up short was Venezuela, which has come under fire from a number of global rights groups for a deteriorating record under President Hugo Chavez.
Iraq, whose rights performance has come under renewed UN criticism following the 2003 US-led invasion that toppled Saddam Hussein, also failed to win a seat.
New criteria
Rights champions generally agree the new membership criteria are more stringent for the new body than for the old.
Election is by secret ballot and governments must undergo regular reviews of their domestic rights records while serving on the council.
Despite the inclusion of rights abusers, UN chief Kofi Annan welcomed the new council's election and the high rate of participation.
"He believes that this demonstrates a widely shared commitment to replace the previous Commission on Human Rights with a body that can work more effectively, and can embody human rights ideals with more credibility," said Mr Annan's spokesman, Stephane Dujarric.
The Human Rights Commission had been elected by a recorded vote of the 54-nation Economic and Social Council and most contenders ran unopposed after nomination by regional blocs.
The commission was shut down after a number of rights-abusing nations won seats and began to work together as a bloc to defeat critical resolutions against any one of them.
Vying for the council's 47 seats were 63 announced candidates, down from 64 on Monday after Kenya withdrew from the race.
That left Africa with just 13 candidates for its 13 seats, the sole region where there was no competition for spots.