The parliament re-elected six out of seven members of the Federal Council, maintaining Bern's previous power share among five of the country's political parties.
Finance Minister Eveline Widmer-Schlumpf of the centre-right Conservative Democrats held onto her seat and was selected to replace outgoing leader, Social Democrat Micheline Calmy-Rey, as president for the coming year.
The cabinet vote was a blow for the far right Swiss People's Party (SVP), which had been eager to boost its representation in government given that it is the country's largest political party.
It has just one seat on the Federal Council while smaller parties have two.
Widmer-Schlumpf, 55, was elected to the cabinet as an SVP member in 2007 but following a split she and other parliamentarians went on to form their own Conservative Democrats.
Thanks to her popularity she not only remains in government but won the top post, even though her party is too small to hold a ministerial portfolio.
The presidency is rotated each year among members of the cabinet and it is a largely symbolic role.
Following the vote SVP lawmaker Hans Fehr said the traditional power share agreement was "broken" while other parties voiced their support for Widmer-Schlumpf's re-election.
"It's good news for Switzerland's stability," said Christian Democrats head Christophe Darbelley.
Conservative Democrat president Hans Grunder said he was "relieved and very happy" with the outcome.
"It's a good sign for the next four years when many challenges await us," said Grunder.
The new government enters into office amid concerns over a slowing economy.
While Switzerland is relatively cushioned against the kind of debt problems that have beset eurozone nations, it is suffering from the fallout.
Its economy is highly dependent on exports, which are suffering as demand drops in Europe.
This is exacerbated by the relative strength of the Swiss franc against the euro and the dollar.
The government on Tuesday cut its 2012 growth forecast to 0.5 percent from 0.9 percent, citing the eurozone crisis as a factor.
Calmy-Rey's seat on the cabinet was filled by fellow Socialist Alain Berset following the Federal Assembly vote.