One of Thomas' top aides, Lisa Aubuchon, was also disbarred for her role in the misconduct. A second aide, Rachel Alexander, had her law license suspended for six months.
The punishments are scheduled to take effect May 10. All three are expected to appeal the ruling.
Thomas blasted the ruling afterward, saying it was another step in the longstanding conspiracy against him.
"Today, corruption has won and justice has lost," he said, according to the Arizona Republic. "The political witch hunt that's just ended makes things worse by sending a chilling message to prosecutors: Those who take on the powerful will lose their livelihood."
The decision was long-awaited for many who follow the ongoing Arizona drama in which Arpaio is a central figure.
Thomas spent six years at Arpaio's side as the top prosecutor in Maricopa County, Ariz., which encompasses Phoenix and most of its sprawling suburbs.
A longtime immigration hardliner, he was first elected to the office in 2004 and won reelection in 2008. Thomas resigned his seat to run for state attorney general in 2010 amid the conservative wave, but he lost in the Republican primary and seemed to drop out of politics after that.
Politically, Thomas and Arpaio were almost inseparable during their years as the top law enforcers in Maricopa County. They supported each other on almost every issue and often found themselves locked together in heated battles with judges and other local government officials.
Those battles were ultimately what led to the ethics case against Thomas.
Investigators with the State Bar of Arizona said somewhere along the way he became obsessed with his political enemies. He turned disagreements over policy into a full-fledged attempt to see his opponents jailed and disgraced.
With Arpaio's help, investigators said, Thomas used the powers of his office to target his opponents with criminal investigations. He had some arrested and some charged with crimes. The evidence he and Arpaio used in the process was often questionable. The charges rarely stuck.
Throughout it, Thomas and Arpaio said that they were on a mission to root out corruption in local government. When ethics investigators came calling several years ago, Thomas said he was the victim of a witch hunt by the local establishment. He said it was part of a conspiracy to maintain the status quo.
Presiding Disciplinary Judge William O'Neil announced the decision Tuesday morning, Arizona time, from the bench of the state Supreme Court. He said the panel sided with the Thomas and his former aides on a few of the 33 charges against them. But he said there was "clear and convincing evidence" that they violated the rest.
One key ruling by the panel was that Thomas and Aubuchon likely committed crimes, including perjury, during their crusade.
Fallout from the feud doesn't end with the ethics investigation. A federal grand jury is believed to still be looking at possible criminal charges against Thomas and Arpaio on allegations that they abused their powers.
Read the ruling against Thomas, Aubuchon and Alexander: