A test of the metre-long core was matched with a geochemical study of the standing megaliths.
Archaeologists pinpointed the source of the stones to an area 15 miles (25km) north of the site near Marlborough.
English Heritage's Susan Greaney said the discovery was "a real thrill".
The seven-metre tall sarsens, which weigh about 20 tonnes, form all fifteen stones of Stonehenge's central horseshoe, the uprights and lintels of the outer circle, as well as outlying stones.
The monument's smaller bluestones have been traced to the Preseli Hills in Wales, but the sarsens had been impossible to identify until now.
The return of the core, which was removed during archaeological excavations in 1958, enabled archaeologists to analyse its chemical composition.
No-one knew where it was until Robert Phillips, 89, who was involved in those works, decided to return part of it last year.
Researchers first carried out x-ray fluorescence testing of all the remaining sarsens at Stonehenge which revealed most shared a similar chemistry and came from the same area.
They then analysed sarsen outcrops from Norfolk to Devon and compared their chemical composition with the chemistry of a piece of the returned core.
English Heritage said the opportunity to do a destructive test on the core proved "decisive", as it showed its composition matched the chemistry of sarsens at West Woods, just south of Marlborough.
Prof David Nash from Brighton University, who led the study, said: "It has been really exciting to harness 21st century science to understand the Neolithic past, and finally answer a question that archaeologists have been debating for centuries.
Never be afraid to try something new…
An amateur built the Ark that lasted forty days and forty nights; professionals built the Titanic that sank.