"This is a very important day for fairness, for justice, for inclusion," said Gov. Parris Glendening, who has backed the bill.
The bill would ban discrimination based on sexual orientation in the areas of housing, public accommodations and employment.
Mooney, R-Frederick/Washington, has argued that the bill gives "special rights" to people who choose a gay lifestyle.
Mooney criticized Glendening for using the power of his office over the budget, state appointments and redistricting to get his way.
"He brags about taking our tax dollars and twisting our arms to vote for things like this," he said.
Glendening said he wouldn't be an effective governor if he didn't use the power of his office to further his agenda.
But in the case of the gay rights bill, Glendening said he didn't have to offer lawmakers any special favors.
"I tried to persuade, argue, I tried to enlighten. We did not use any resources of the office other than my personal persuasion," Glendening said.
The arguments didn't persuade Sen. Donald F. Munson, R-Washington, who voted against the bill and in favor of Mooney's amendments.
After the vote, Munson declined to elaborate on his opposition. He would only say that the majority of the Senate had spoken.
Monday night, Mooney had hoped to keep the filibuster going long enough to convince fellow lawmakers to adopt a religious freedom amendment.
The amendment, which died on a 26-19 vote, would have exempted people acting on religious beliefs from the ban.
"Maryland has always protected religious freedom. An individual should not be forced to condone values they don't believe in," Mooney argued.
Gay rights supporters said the amendment would gut the bill. And Sen. Delores Kelley, D-Baltimore, argued it was a question of separation of church and state.
"Some of the worst atrocities that have ever been perpetrated were in the name of religion," she said.
Debate on the issue of gay rights was cut off when the Senate voted 32-13 to end the filibuster.
"Those that support discrimination stood up on the floor and got counted. And they were in the minority," said Michael Morrill, spokesman for Gov. Parris Glendening.
The House Judiciary Committee will vote on the bill as soon as today, which means the full House of Delegates may take a final vote later this week.
Two years ago, five of the six Washington County lawmakers voted against the bill. Del. Sue Hecht, D-Frederick/Washington, was the only supporter.
Del. Robert A. McKee, R-Washington, said he hadn't decided how he'll vote this time.
The bill is somewhat different this time because it doesn't ban discrimination against transgendered people. It also makes exceptions for religious organizations, the Boy Scouts and Girl Scouts and landlords who rent rooms in their own homes.