James Brady, Andrew Rossig and Marko Markovich jumped off the tallest US building in 2013, when it was still under construction.
But their lawyers fought the serious charge of felony burglary by persuading the jury they did not intend to commit another crime on the premises.
It caused embarrassment to authorities.
Officials were put on the defensive by the security breach, which came days after a teenager had also gained access.
The jury in state Supreme Court in Manhattan reached the verdicts against 33-year-old Brady, 34-year-old Rossig and 28-year-old Markovich after deliberating for four days.
Defence lawyers said the legal definition of burglary - being in a building illegally with the intention of committing another crime - had not been met.
"We always felt that the felony did not apply, and the jury agreed," said Markovich's lawyer, Joseph Corozzo.
Another lawyer, Andrew Mancilla, called the verdict "a huge relief". But he added: "It's just a shame so much of the taxpayers' money had to be wasted."
But Manhattan District Attorney Cyrus Vance said the jump had been "reckless and illegal" and the trio "took pride in their perceived accomplishment, and seemed to relish evasion of authorities".
All three will be sentenced in August. They could be jailed for up to a year.
Three men who used parachutes to jump from the top of One World Trade Center in New York have been convicted of reckless endangerment.