It is thought the shafts served as a boundary to a sacred area or precinct associated with the henge.
Experts from the University of St Andrews were joined by counterparts from institutes including Birmingham, Warwick, the University of Wales Trinity Saint David, and the Scottish Universities Environmental Research Centre at the University of Glasgow.
Dr Richard Bates, of the university's School of Earth and Environmental Sciences, said: "Yet again, the use of a multidisciplinary effort with remote sensing and careful sampling is giving us an insight to the past that shows an even more complex society than we could ever imagine.
"Clearly sophisticated practices demonstrate that the people were so in tune with natural events to an extent that we can barely conceive in the modern world we live in today."
Tim Kinnaird, of the same school, said: "The sedimentary infills contain a rich and fascinating archive of previously unknown environmental information.
"With optically stimulated luminescence profiling and dating, we can write detailed narratives of the Stonehenge landscape for the last 4000 years."
The announcement of the discovery comes after the Summer Solstice, which took place online this year with the annual gathering cancelled due to coronavirus.
English Heritage has provided access to the event since 2000 but warned visitors not to travel to the 3000 BC Neolithic monument this year.
Dr Nick Snashall, National Trust archaeologist for the Stonehenge and Avebury World Heritage Site, hailed the "astonishing discovery".
He said: "As the place where the builders of Stonehenge lived and feasted Durrington Walls is key to unlocking the story of the wider Stonehenge landscape, and this astonishing discovery offers us new insights into the lives and beliefs of our Neolithic ancestors.
"The Hidden Landscapes team have combined cutting-edge, archaeological fieldwork with good old-fashioned detective work to reveal this extraordinary discovery and write a whole new chapter in the story of the Stonehenge landscape."
