Chief Justice John Roberts jumped on the idea of a rapid shift in opinion to suggest that perhaps gays and lesbians do not need special protection from the court.
"As far as I can tell," Roberts said, "political leaders are falling all over themselves to endorse your side of the case."
The justices stepped into the dispute after lower federal courts ruled against the measure.
The DOMA argument followed Tuesday's case over California's ban on same-sex marriage, a case in which the justices indicated they might avoid a major national ruling on if gays and lesbians have a right to marry. Even without a significant ruling, the court appeared headed for a resolution that would mean the resumption of gay and lesbian weddings in California.
Supreme Court arguments are the most visible part of the justices' consideration of the cases before them, but they often play a relatively small role in rulings compared to the mountain of legal briefs that are filed in the weeks leading up to the public sessions.
Lawsuits around the country have led four federal district courts and two appeals courts to strike down DOMA's Section 3, which defines marriage. In 2011, the Obama administration abandoned its defense of the law but continues to enforce it.
The change in position led the court to consider the related questions of if the House Republican leadership can defend the law in court because the administration decided not to, and if the administration forfeited its right to participate in the case.
Roberts and Scalia seemed most interested in this sort of outcome, and the chief justice offered perhaps the most pointed comment of the day when he wondered why Obama continues to enforce a law he believes is unconstitutional.
"I don't see why he doesn't have the courage of his convictions and execute not only the statute but do it consistent with his view of the Constitution, rather than saying, 'Oh, we'll wait till the Supreme Court tells us we have no choice,'" Roberts said.
If the Supreme Court finds that it does not have the authority to hear the case, Windsor probably would still get the $363,000 estate tax refund for which she sued because she won in the lower courts. However, there would be no definitive decision about the law from the nation's highest court, and it would remain on the books.
Windsor, who goes by Edie, married Thea Spyer in 2007 in Canada after doctors told them that Spyer would not live much longer. Spyer, who suffered from multiple sclerosis for many years, died in 2009 and left everything she had to Windsor.
There is no dispute that, if Windsor had been married to a man, her estate tax bill would have been zero. Windsor was in court Wednesday, where she received a hug from House Democratic Leader Nancy Pelosi before the argument started.
The 2nd U.S. Circuit Court of Appeals in New York agreed with a district judge that the provision of DOMA deprived Windsor of the constitutional guarantee of equal protection of the law.
Reflecting the high interest in the cases, the court released an audio recording of Wednesday's argument, just as it did Tuesday for that day's proceedings.
A somewhat smaller crowd gathered outside the court Wednesday, mainly gay marriage supporters who held American and rainbow flags.
"Two, four, six, eight, we do not discriminate," a group chanted at one point.
"If this isn't the time, when is the time? When does equality come into play?" asked Laura Scott, 43, of Columbia, Md.
Wednesday's case is U.S. v. Windsor, 12-307.