Collins, sticking with the GOP's line that the Senate first should resolve the issues of the Bush tax cuts and government funding before proceeding to any other matters, said the stand-alone bill can pass if it is brought to the floor at the right time.
"As long as the priority items -- taxes and funding -- have been completed, I believe that the votes are there," Collins said.
Both she and Lieberman ripped Reid for holding today's vote, saying they were "disappointed" in him.
"There was a clear path forward to victory on this issue and to consideration of this bill, and for the life of me I cannot understand why the majority leader chose not to take it," said Collins.
It will be far from easy with such a full slate of issues to resolve, but despite today's setback, a stand-alone repeal of "don't ask, don't tell" still could happen before year's end.
If a free-standing bill were to pass the Senate, it still would have to pass the House of Representatives, which could be a challenge because Republicans will gain control of the House next month.
The debate and vote on gays in the military is competing for time on the Senate schedule for the remainder of a lame-duck session that is expected to include addressing the Bush tax cuts, government funding and the START treaty with Russia.
Complicating matters further was Senate Republicans' stated refusal earlier this month not to vote for any measures until taxes and funding are resolved, a move denounced by Reid as merely an "artificial roadblock" designed to obstruct Democratic efforts.
"Putting up these artificial roadblocks is foolishness," Reid said. "What in the world do they accomplish by saying we're not going to allow you to do the START treaty, the defense authorization bill, until the tax bill is complete and spending is done?"
Today's vote marked the second time this year that lawmakers in the upper chamber have acted on the controversial issue.
On Sept. 21, Senate Republicans, led by Sen. John McCain, R-Ariz., shot down the bill. Democrats needed 60 votes to advance the bill over a GOP filibuster, but only secured 56 votes.
However, one of the no votes was from Reid, who only took that vote in a procedural move to allow him to bring up the measure again at a later date. Another one of those no votes was from Sen. Mark Pryor, D-Ariz., who announced Wednesday that he would now support the effort to change the policy.
"I have now carefully reviewed all of the findings, reports and testimony from our armed forces on this matter and I accept the Pentagon's recommendations to repeal 'don't ask, don't tell,'" Pryor said. "I also accept the secretary of defense and chairman of the Joint Chiefs' commitment that this policy can be implemented in a manner that does not harm our military's readiness, recruitment, or retention."
The controversial policy that prohibits gays serving openly in the military has been in effect since 1993. The House already has approved a conditional repeal of it, leaving its fate in the hands of the Senate.
ABC News' Huma Khan and Ariane de Vogue contributed to this report.