The USS Port Royal was pulled off a rock and sand shoal at around 2 a.m. after crews removed about 500 tons of water and 100 tons of anchors and other equipment to lighten the vessel, the Navy said in a statement.
The removal by a salvage ship and seven tug boats took about 40 minutes.
The area was to be examined to determine if the ship leaked any fuel, said Coast Guard Capt. Barry Compagnoni.
The Port Royal was being towed to Naval Station Pearl Harbor for inspection.
The guided missile cruiser ran aground Thursday just off Honolulu International Airport. It was visible to everyone flying in and out of Oahu and also was in clear view from a nearby public beach park.
The ship ran hit bottom while sailors, contractors and shipyard personnel were being unloaded. The 15-year-old Port Royal usually has about 24 officers and 340 enlisted sailors on board.
Efforts to refloat the vessel during the weekend were unsuccessful. On Sunday, the Navy was able to turn the ship more than 20 degrees but still couldn't pull it free.
The Navy has not discussed what might have caused the grounding. An investigation was expected once the ship returns to shore.
The vessel had just finished its first day of sea trials after wrapping up a four-month routine maintenance stay at Pearl Harbor Naval Shipyard.
The Pearl Harbor-based Port Royal, one of the Navy's most advanced ships, is equipped with Aegis ballistic missile tracking technology.