Senate Republicans confirmed Susan Monarez, the acting director of the Centers for Disease Control and Prevention and a supporter of Covid vaccines, as the permanent leader of the agency, cementing President Trump’s second pick for the job after he withdrew his first nominee just hours before his confirmation hearing earlier this year.

Dr. Monarez, an infectious-disease researcher, is the first nonphysician to lead the C.D.C. in more than 50 years. Her confirmation, in a 51-to-47 party-line vote in the Senate, comes as Robert F. Kennedy Jr., the health secretary, has overseen aggressive cuts to the agency — many of which were later reversed — and after he gutted an influential committee that recommends which vaccines Americans should get.

Dr. Monarez, 50, assumed the acting director position a few days after Mr. Trump took office in January, leaving her perch as deputy director of a new federal biomedical research agency created during the Biden administration.

Dr. Monarez was expected to serve until Mr. Trump’s first choice for the job, Dr. Dave Weldon, a former Republican congressman, could be confirmed. But after Mr. Trump decided to withdraw the nomination, Republican aides in the Senate said that Dr. Weldon had failed to impress them with a plan for the agency.

Dr. Weldon blamed two Republican senators — Susan Collins of Maine and Bill Cassidy of Louisiana — for turning against him.

Some experts said Dr. Monarez was a sharp contrast to Dr. Weldon, whose skeptical views on childhood vaccines aligned with those of Mr. Kennedy and raised alarm in the medical community. Dr. Monarez, in contrast, is a biosecurity expert who endorsed the Covid vaccines, and her selection was seen as signaling a growing impatience with anti-vaccine sentiment.