Health insurers must immediately start paying for long-term antibiotic treatment for Lyme disease after the Legislature overrode a veto by Governor Charlie Baker in the waning hours of the session Sunday night.

In other health-related actions, the Legislature restored a long-sought wage increase for nursing home workers and voted to require health insurers to cover treatment for a side effect from HIV drugs.

The mandate on Lyme disease coverage came despite objections from dozens of medical specialists who said such treatment is ineffective at best — and sometimes harmful. The governor had proposed, instead, that the Executive Office of Health and Human Services hold listening sessions about the appropriate treatment of Lyme disease.

Representative David P. Linsky, a Natick Democrat and proponent of the Lyme disease bill, said an emergency provision directed that the law go into effect at 11:58 p.m. Sunday, when the Senate voted, 37 to 1, to override the governor’s veto. The House had voted earlier to override, 153 to 3, Linsky said.

“The members of the Legislature responded to the stories from constituents all over the state whose lives and families have been negatively affected by Lyme disease,’’ Linsky said.

Asked why the concerns of medical specialists carried so little weight, Linsky said, “It’s not the role of the Legislature or the governor to determine what the appropriate course of treatment is for Lyme disease.’’

Dr. James S. Gessner, president of the Massachusetts Medical Society, which opposed the legislation, said in a statement: “It is the medical profession’s position that coverage of treatments for any condition be medically necessary and evidence-based.’’

Massachusetts had the nation’s third-highest incidence of Lyme disease in 2014, with 5,600 confirmed and suspected cases.

Sheila M. Statlender, a Newton psychologist who advocated for the bill, called the override vote a “historic, landslide victory,’’ but added, “It’s our hope that the bitter polarization will end. That includes not only people talking nice, but really taking a look at the emerging science and trying to have open minds.’’

Some people infected with Lyme disease continue to have symptoms after the standard two to four weeks of antibiotic therapy, for reasons that are poorly understood. Most doctors suspect the continuing problems, which include muscle aches, fatigue, and mental fogginess, result from damage to tissue or to the immune system.

But some patients believe the bacteria survive after treatment, and a minority of doctors are willing to provide the unorthodox treatment of months of oral or intravenous antibiotics. That treatment puts patients at risk of blood clots, blood-stream infections, gallbladder problems, and intestinal woes.

The Lyme coverage requirement doesn’t apply to the 60 percent of insured people who get health insurance from large employers who self-insure. These employers, who directly provide coverage to workers rather than buying a health plan from an insurer, are exempt from state rules.

Mandated insurance benefits disproportionately burden small businesses, said Lora M. Pellegrini, president of the Massachusetts Association of Health Plans, a trade group for health insurers. And these new expenses are coming at a time when businesses need more flexibility to better control costs, she said.

On the nursing home wage provision, the Legislature restored $35.5 million in pay raises for low-paid nursing aides. Baker had slashed roughly half the money.

Leaders of 1199SEIU United Healthcare Workers East, a union that represents many nursing home workers, noted that the money was not dependent on state revenue, and was instead to be raised through a “user fee’’ on the roughly 400 nursing homes in Massachusetts.

The union prevailed as lawmakers Sunday restored the full raise, including a provision calling for an audit to ensure that nursing homes pass the money to workers. The audit is due to the Legislature by Jan. 30.

“Quality care is directly linked to quality jobs, and this funding is essential to ensuring quality long-term care for seniors, people with disabilities, and their families,’’ said Tyrék D. Lee Sr., SEIU’s executive vice president.

The legislation affecting HIV patients still needs the governor’s signature.

The bill, which advocates said was the first of its kind in the country, would require insurance and Medicaid coverage for the treatment of HIV-related lipodystrophy, a condition of painful, abnormal changes in body shape.

Lipodystrophy is believed to be a side effect from the first wave of lifesaving HIV medications. It can cause fat growths on the back of the neck that press on the spine, or fat loss in the face or limbs.

The drugs blamed for these problems have since been supplanted by better medications, but a few hundred people in Massachusetts who took them in the 1990s still suffer from the disfiguring side effects.

Most health insurers consider lipodystrophy treatment to be cosmetic, and thus not covered.

If Baker signs the bill, the new mandate will increase a typical person’s health insurance premium by one to 10 cents a year, according to the state’s Center for Health Information and Analysis.

Kay Lazar of the Globe staff contributed to this report. Felice J. Freyer can be reached at felice.freyer@globe.com. Follow her on Twitter @felicejfreyer.