After suffering from an apparent malfunction in one of its grid fins, the booster fell into the sea - but remained intact and will be retrieved.
A SpaceX commentator called it a "bummer", but noted it was secondary to the main mission of getting the Dragon capsule to orbit.
SpaceX quickly cut the live feed from the rocket as it began to spin out of control.
SpaceX on Wednesday blasted off its unmanned Dragon cargo ship, loaded with supplies, science experiments and food for the astronauts living at the International Space Station but failed to successfully land its booster afterward.
The first stage of a SpaceX Falcon 9 rocket topples onto its side after splashing down in the ocean during a failed landing attempt on December 5, 2018. The launch itself was a success, but landing the rocket for reuse didn't go as planned.
But the tall portion of the rocket missed its goal of securing an upright landing on the solid ground at Cape Canaveral's Landing Zone 1. As promised, the company shared a video showing the rocket stabilizing as it approached the ocean, where it gracefully landed and then promptly tipped over, floating in the water.More news: Saudi Arabia works on convincing Russian Federation to join oil cuts
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Falcon 9 is now the only reusable rocket booster, which is a major selling point for SpaceX. It appeared to be undamaged and was transmitting data, Musk said, adding that a recovery ship was sent to retrieve it.
Altogether, the company has recovered 32 boosters following liftoff - 33 once this one is towed back, said Hans Koenigsmann, a SpaceX vice-president.
Koenigsmann said the booster deliberately avoided land after sensing a problem, a built-in safety feature, and even managed to touch down upright in the Atlantic, atop its landing legs. His interest in space, and his background in journalism and public relations suit him for his focus on research and development activities at NASA Glenn Research Center, and its Plum Brook Station testing facility, both in northeastern Ohio. SpaceX redesigned those COPVs after a September 2016 pad explosion in order to meet NASA safety requirements for future commercial crew missions.
Today's SpaceX launch will use a new Block 5 booster. "It knows where buildings are, so it's pretty smart in that aspect", he said of the landing system on the booster.
The mission is SpaceX's 16th for NASA, as part of a long-term contract to ferry supplies to space.