It appeared to be undamaged and was transmitting data, Musk said, adding that a recovery ship was sent to retrieve it.
Even though it didn't manage to get back to its landing pad, the rocket had enough smarts on board to stabilise itself before it fell into the water.
The rocket engines compensated somewhat for the spin, and by the time the rocket hit the water, its fin had emerged.
The CRS-16 mission launched supplies to the ISS on Wednesday, but the booster headed for the landing pad missed and landed in the water instead, ending SpaceX's ideal record of 12 previous successful landings.
SpaceX commentator John Insprooker said, "We have done an excellent lift".
Today's incident marks the first time the Falcon has failed to land at designated spot (solid ground) ever since SpaceX began recovering boosters.
Later it became known that the ship was successfully launched into orbit.
Company CEO Alan Musk wrote on Twitter, "The grid in hydraulic pump stops, that's why the Falcon could only land in the sea".
"Dragon, you saw separate, and now the solar arrays coming out".
This was SpaceX's sixteenth supply mission to the International Space Station.
The Dragon is carrying more than 56-hundred pounds of supplies and payloads to the International Space Station, including critical materials to directly support more than 250 science and research investigations.
SpaceX's successful Falcon 9 rocket launch proved to be quite a spectacle for viewers and was considered a success despite the lost booster. The mice and their habitat were loaded into spacecraft shortly before launch, but the spoiled food had to be replaced ahead of launch.