Yankees general manager Brian Cashman said that Hughes had an epidural shot administered in response to the flare-up, believed to stem from a herniated disc the hurler suffered in 2004.
Cashman said that the team considers the situation "not serious" and that it would have normally resolved itself over time, but the Yankees went for a quicker fix with the postseason looming.
"My conversations with Phil and [team physician] Dr. Chris Ahmad would lead me to feel really good that this is not a big issue," Cashman said.
Hughes complained of back spasms after throwing a bullpen session on Friday in Toronto, and had his start scheduled for Monday pushed back. He was unable to pitch on Wednesday either, with Hector Noesi getting the spot start nod against the Rays.
"We believe he'll be fine. We believe he'll still pitch for us," Cashman said.
Hughes is expected to start one of the games in the season's final series of the year next week against the Rays at Tropicana Field.
Cashman said that he was not sure if the Yankees would be looking at Hughes -- 5-5 with a 6.00 ERA in 15 games (14 starts) -- to start or relieve when the team begins their postseason run.
"We really haven't had those types of meetings, in terms of role," Cashman said. "I think he'll be able to start or relieve, if that's what we want."