Jones made the announcement Thursday afternoon on the duo's web site.
"God has been on my heart to announce and make public that I have entered a rehabilitation and treatment facility to address issues related to alcohol and substance abuse," Jones wrote in the statement to his fans.
Jones' girlfriend and singing partner, Meghan Linsey, announced Sept. 23 that the duo would cancel a handful of shows because the 31-year-old was unable to perform, but didn't specify why. Linsey began playing Steel Magnolia's scheduled tour dates alone on Sunday.
The duo released its self-titled debut album earlier this year and is nominated for the vocal duo of the year award at the Country Music Association Awards in November.
Jones and Linsey have one of those only-in-Nashville stories. They both came to Music City with dreams of a singing career and met in a karaoke bar in Printers Alley. They teamed to win the CMT singing contest "Can You Duet" in 2009, earning a contract with Big Machine Records.
Steel Magnolia's boy-girl lineup is a rare one in Nashville and they have further distinguished themselves with a unique soaring blend of country and R&B harmonies.
Their first single, "Keep on Lovin' You," reached No. 4 on the Billboard Country chart in 2009. The self-titled debut album opened at No. 7 on the all-genre Billboard 200 and No. 3 on the country charts.
It's unclear how long it will take Jones, an Illinois native, to return to the stage or how many shows Linsey, originally from Louisiana, will play alone. The duo is scheduled to join Reba McEntire's All The Women I Am Tour on Oct. 6 in Moline, Ill.
Jones thanked his family, friends and label and management teams for their support and active role in his recovery.
"Hundreds of thousands of people in the world struggle with these battles daily, therefore I am sincerely grateful for all thoughts and prayers at this very poignant juncture in my life and career," Jones said.