Cmdr. Christy Hagen, spokeswoman for the U.S. Pacific Fleet's submarine force, says Cmdr. Nathan Sukols and Lt. Cmdr. Lauren Allen were relieved after a disciplinary hearing in Bahrain on Sunday.
Hagen cited a lack of confidence in the pair's leadership, but gave few details. Both have been assigned to administrative duties.
On Jan. 10, the Jacksonville hit a vessel that kept moving and showed no signs of distress afterward. A periscope was damaged, and has since been repaired.
The Navy couldn't determine the boat's purpose or country of origin before it moved on.
No one was injured.