The 21-year-old was in line for his senior international debut after impressing in his first four appearances since joining United from Crystal Palace in a £50 million ($60 million) deal in June.
“Aaron Wan Bissaka has withdrawn from the England squad,” the English Football Association said in a statement.
“The Manchester United right-back has returned to his club due to a back issue.
“With Trent Alexander-Arnold and Kieran Trippier already included in Gareth Southgate’s now 24-man squad, no replacements are planned.”
England are already well on course to qualify for next year’s European championships after thrashing the Czech Republic and Montenegro in their opening two qualifiers.
Wan-Bissaka was just one of four uncapped players named in Southgate’s squad last week as the England boss plans on giving a chance to a host of young players with an eye already on next summer.