County offices in Philadelphia stayed open late to handle marriage applications, while officials in Pittsburgh were closed for election day but accepting them online.
Couples must wait three days before getting married, unless a sympathetic judge grants a waiver.
Joe Parisi told his partner to "jet out of work" and get to Philadelphia City Hall.
"We didn't want to take the chance of having this be challenged, and missing out on our opportunity," said Parisi, 30, of Philadelphia, who plans to marry 28-year-old Steven Seminelli. They were among the first to get a license Tuesday afternoon, just hours after Jones' ruling.
Jones also ordered Pennsylvania to recognize same-sex marriages performed elsewhere.
"It's everything we had hoped for," said Witold "Vic" Walczac, legal director of the American Civil Liberties Union of Pennsylvania, which pursued the case. "There's nothing that the government can do that's more intrusive than standing in the way of two people who love each other and want to get married."
State marriage bans have been falling around the country since the U.S. Supreme Court last year struck down part of the federal Defense of Marriage Act. If Jones' decision stands, Pennsylvania would become the 19th state to legalize gay marriage, and 43 percent of Americans would live in a state with full marriage equality, according to the advocacy group Freedom to Marry.
The ACLU had argued that the bans deprive same-sex couples and their families of the legal protections, tax benefits and social status afforded to married couples.
Corbett's office was left to defend the law after Attorney General Kathleen Kane, a Democrat, refused to do so.
"We're currently reviewing all the legal issues presented in the opinion," said Joshua Maus, a spokesman for Corbett's legal office.
The Pennsylvania lawsuit, filed July 9, was the first known challenge to the state ban. At least five later test cases emerged, including one over a suburban county's decision last year to issue 174 marriage licenses to same-sex couples, before a court order to stop doing so. Officials in Montgomery County were trying Tuesday to have that order lifted.
Oregon became the 18th state to recognize same-sex marriage on Monday, when jubilant couples began applying for marriage licenses immediately after U.S. District Judge Michael McShane issued a ruling that invalidated that state's voter-approved same-sex marriage ban.
Also Monday, a federal judge in Utah ordered state officials to recognize more than 1,000 gay marriages that took place in the state over a two-week period before the U.S. Supreme Court halted same-sex weddings with an emergency stay.
Jones, a Republican and an appointee of former President George W. Bush, was previously known for a 2005 decision in which he barred a Pennsylvania school district from teaching "intelligent design" in biology class, saying it was "a mere re-labeling of creationism."