Temer has been Rousseff's deputy since she took office in 2011, becoming the first woman to hold the position of president.
But their relationship has deteriorated, with Rousseff now referring to him as a "traitor," and the PMDB withdrawing from the coalition government last month. Brazil was one of the world's fastest-growing economies until a few years ago, but is now in the midst of one its worst recessions in decades.
Some 11 million Brazilians cannot find a job. Temer, who is perceived as more market-friendly, has called for investor calm. He said he wants to slim down the number of cabinet positions and make appointments from across the political spectrum.
Rousseff is accused of tampering with figures to disguise the size of Brazil's budget deficit during her 2014 re-election campaign. She has denied any wrongdoing.
Ahead of the Senate vote, local media reported that Rousseff had cleared her personal effects from the presidential office.
Bitter political rival Eduardo Cunha, who was the president of Brazil's lower house, launched the process to impeach Rousseff in December.
The chamber voted in favour of her impeachment in April, sending the issue to the Senate upper chamber.
Cunha was suspended last week on allegations he was obstructing a corruption investigation against himself.
In a last-ditch effort to save her presidency, Rousseff appealed to the Supreme Court this week to block the Senate vote, arguing that Cunha had abused his position of power to seek "revenge".
The court rejected her appeal.
Mass street protests broke out in the country last year, reflecting the anger of Brazilians at the government's inability to improve economic conditions and widening corruption scandals that have left around 60 per cent of the 594 members in the National Congress.
The biggest of all the scandals involves state-run Petrobras.
Bribes totalling billions of dollars are alleged to have been paid in the awarding of dozens of contracts by the oil giant to construction companies. Some of the money was then shared with politicians from several political parties.
Rousseff was chairwoman of the Petrobras board between 2003 and 2010, when the kickback schemes were said to have taken place.
She denies having had any knowledge of wrongdoing and has not been charged in the case.
She has been mired in the scandal, however, helping to drive her popularity rating down to around its current 14 per cent.
- AAP