The moon is a multibillion-year-old library of impact events, with fresh collisions still taking place frequently.
However, the meteorite impact was seen many times before this, but not during the eclipse.
Jose Maria Madedo from the University of Huelva in Spain has confirmed that it is indeed a meteorite.
The eclipse was dubbed the "super blood wolf moon" by scientists because the moon appeared bigger due to its closeness to Earth and its striking, unusual color.
Such a scene has been long-sought by astronomers, but proved elusive until now, even with the frequency of lunar eclipses.
Madiedo said it's the first impact flash ever seen during a lunar eclipse, although such crater-forming impacts are common, the Associated Press reported.
He doubled the number of telescopes the program usually has pointed at the Moon - from four to eight - and crossed his fingers.
The super blood wolf moon eclipse was a wonder of nature which entraced the world - and sent apocalypse prophets into paroxysms of fear. Their software immediately logs the flashes and identifies their exact location on the lunar surface to an accuracy of about 0.001 seconds.
"I am really happy, because I think that the effort was rewarded", he said.
The MIDAS survey is a Moon-watching that scours video of its surface in the hopes of detecting the tiny flashes associated with meteorite impacts.
The impact has been captured on video for the first time in history during a total lunar eclipse. "I was really exhausted when the eclipse was over".
The lunar strikes often come in the form of "musket ball" sized rocks no more than a few dozen grams or so in mass, according to Robert Frost, instructor and flight controller in the Flight Operations Directorate at NASA.
The next lunar eclipse will only be a partial lunar eclipse, visible from South America, Europe, Africa, Asia and Australia.