The defender, 29, was stretchered off during Tuesday night's defeat against Bradford and a scan on Wednesday revealed the damage.
A statement on the club's website read: "It has been confirmed that Danny Woodards damaged his anterior cruciate ligament during Tuesday night's defeat to Bradford.
"The defender will undergo an operation tomorrow, and will be out for up to nine months.
"It is the second serious injury for Danny, who last year broke his ankle during the final match of the season."
After recovering from that setback, Woodards went on to make 22 appearances this term but is now not expected to feature again until 2014.
Rovers have already lost Matt Harrold, Garry Kenneth and Seanan Clucas to cruciate injuries this campaign, with the number of long-term casualties this season now standing at eight.
Boss John Ward told BBC Radio Bristol: "The injury list is ongoing and pretty depressing when you look at it.
"You talk to Phil Kite, who's been physio for a long time, and it's a new phenomenon for him, too.
"He's never seen that kind of injury list. For us to be in the good league position we are now in shows the effort from the club."