The Senate voted on Saturday to confirm Kristi Noem as homeland security secretary, putting a former South Dakota governor in charge of the department at the heart of President Trump’s agenda to crack down on immigration.

The vote was 59 to 34.

Ms. Noem, a longtime ally of Mr. Trump who was once seen as a contender to be his running mate, issued a statement on Saturday thanking him and vowing to “work to make America SAFE again!”

She takes charge of a sprawling agency that runs the nation’s immigration system — including Customs and Border Protection and Immigration and Customs Enforcement — and that leads counterterrorism efforts. The Homeland Security Department also oversees the Secret Service, the Coast Guard and the Federal Emergency Management Agency. (In recent days, Mr. Trump has suggested disbanding FEMA.)

Ms. Noem, a former congresswoman and two-term South Dakota governor, has been closely aligned with Mr. Trump on immigration, the issue he says won him the White House.

She has described high levels of immigration to the United States in recent years as an “invasion,” and she has supported restoring a policy that requires asylum seekers to stay in Mexico for the duration of their U.S. cases. The policy, in place during Mr. Trump’s first term, was heavily criticized by Democrats and immigration-rights activists.

As governor of South Dakota, she opposed accepting Afghan refugees after the chaotic American withdrawal from Afghanistan, and she sent members of her state’s National Guard to Texas to address the immigration crisis — a contentious move that Mr. Trump cited in picking her for homeland security secretary.