Two of the prisoners, who had been accused of crimes connected to the Palestinian uprising, decided to remain in the West Bank.
The seven who returned were sent by bus across the Allenby bridge linking Jordan with the Palestinian territories and Israel.
The Israeli cabinet approved their release on Sunday.
The nine men had been serving prison terms from four to eight years for offences that included possessing weapons, inciting public disorder or using firearms against Israeli soldiers during protests in the Palestinian territories.
The release is the culmination of
months of negotiations
"I am happy to be free, but at the same time sad because other Jordanians remain in Israeli detention," Abd al-Basit Dalalsha, one of the freed prisoners, said.
He had been convicted of possessing arms and served half of his eight-year term.
Al-Basit urged his government to consolidate its efforts to win the release of the remaining Jordanians, saying that was a "message from my brothers, the Jordanian prisoners".
Jordan says 15 other citizens remain in Israeli jails and negotiations will continue to win their freedom.
Israel says they are accused of involvement in attacks against its citizens.
Four of them have been convicted of killing Israelis, and Israel refuses to release them.
"I am happy to be free, but at the same time sad because other Jordanians remain in Israeli detention"
Abd al-Basit Dalalsha,
freed from Israeli prison
The families of the seven showered the men with flowers as they alighted from the bus into a VIP lounge on the Jordanian side of the bridge.
Women ululated and men clapped and danced in the street.
"I am very happy to see my son free and alive," Mustafa al-Dabay said weeping as he hugged his son, Ahmad, who served nearly half of his six-and-a-half-year jail term.
Ahmad said he was convicted of being a "suicide bomber". "Thank God for making this day come true," the older al-Dabay said.
The release of the nine is the culmination of months of negotiations with Israel, which is bound by a peace treaty concluded with Jordan in 1994.