The Christian families who own the companies -- Hobby Lobby, a chain of craft stores with 13,000 employees, and Conestoga Wood Specialties, a small Mennonite furniture manufacturer -- say that forcing them to insure certain forms of contraception violates their First Amendment freedom of religion.
The companies say they're protected under the Religious Freedom Restoration Act of 1993, which is designed to prevent laws that place a substantial burden on a person's free exercise of religion.
The three liberal-leaning women on the high court expressed concern that denying female employees access to even some contraceptives is unfair and threatens their health.
"Congress has made a judgment and Congress has given a statutory entitlement [with the Affordable Care Act], and that entitlement is to women and includes contraceptive converge," Justice Elena Kagan said.
"When the employer says, no, I don't want to give that, that woman is quite directly, quite tangibly harmed."
The Affordable Care Act provides for a range of free preventive care, including 20 forms of contraception. The Obama administration has strongly defended the provision, saying it puts women in control of their health care.
Both companies say they are amenable to providing 16 of the mandated forms of contraception. But they oppose emergency contraceptives like the morning-after pill and certain intrauterine devices (IUDs), arguing that life begins at conception and that destroying an already fertilized egg in the uterus is tantamount to abortion.
Solicitor General Donald Verrilli Jr., arguing the case on behalf of the Obama administration, said the companies' abortion position doesn't hold legal water.
"It is their sincere belief and we don't question that," he said. "But I will say … [that] is not the judgment that federal law or state law reflects.
"You've got about 2 million women who rely on the IUD as a method of birth control in this country. I don't think they think they are engaged in abortion in doing that."
But Paul Clement, who is representing the two businesses, told the justices that only family-run companies like his clients — not large corporations — are likely to contest the contraceptive mandate.
"We can talk about the extent and how you'd apply these principles to Exxon, but I think that's just something that's not going to happen in the real world," Clement said.
Kagan suggested the businesses can decide not to provide health care coverage for their employees if they pay a $2,000 per-employee penalty -- a scenario she said would save the companies money. Then, if the companies wanted to ensure their employees had health care, they could raise their salaries so employees can buy private coverage.
"So there is a choice here," she said. "This is not the kind of thing that's going to drive a person out of business. It's not prohibitive."
But Justice Antonin Scalia scoffed at the notion that such a scenario wouldn't be a significant financial burden for the companies.
"It's absurd to say that [the cost] comes out of nowhere," he said.
Justice Sonia Sotomayor questioned whether a ruling in favor of the companies would establish a pathway for other pro-profit entities to ask for a slew of other exemptions on religious grounds for such medical procedures as blood transfusions and vaccinations.
George Washington University law professor Ira Lupu said he expects Justice Anthony Kennedy — often the deciding vote on 5-4 cases — to again cast the swing vote in the ruling, which is expected in June.
"Justice Kennedy is the key to this," Lupu said. "He had questions from both sides, he pressed both sides."
Barbara Green, who co-founded Hobby Lobby with her husband, David, in Oklahoma City in 1972, said the government's position "is out of step with the history of our great nation founded on religious freedom."
"We believe that no American should lose their religious freedom just because they open a family business," she said. "We are thankful that the Supreme Court has heard our case, and we prayerfully await the justices’ decision."
Sen. David Vitter of Louisiana, who collectively wrote with three other Republican senators an amicus brief in support of Hobby Lobby and Conestoga Wood, said the government has no business forcing companies to go against their religious convictions.
"The ability to practice the faith we choose is one of our great constitutional rights," Vitter said. "But with this contraceptive mandate, the Obama administration is stomping on that right."
But women's groups and activists say that women in the workforce — not a for-profit company like Hobby Lobby — would be the true victims should the high court side with the companies.
"To them, it’s a debate about ‘freedom,’ except of course the freedom for women to access care," said Sen. Patty Murray, D-Wash.
Lower courts sided with Hobby Lobby but rejected the claims of Conestoga Wood, a Pennsylvania company that employs 950 people.
The Supreme Court in 2012 upheld the constitutionality of Obamacare's central tenets, including the birth control provisions.
If the justices side with the two companies, the ruling likely would expand on the political rights that businesses won in Citizens United v. Federal Election Commission. In that 5-4 decision, the high court struck down most limits on corporate and union spending in elections on the grounds they violated First Amendment guarantees of free speech.
Since the 2010 ruling, some lower courts have applied the same reasoning to religious beliefs.
This article was originally posted at 1:59 p.m. and has been updated.