Hooker Hartley was injured in England's Six Nations match against Ireland last month and has not played since.
"I'm very disappointed that I will not be available for selection for Saints' remaining Premiership games, as well England's tour to South Africa," Hartley said in a statement.
"It has been recommended by specialists that I take a break this summer and while I find that decision hard to accept, it’s important I listen to that advice."
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England's three-test series in South Africa starts on June 9.
(Reporting by Simon Jennings in Bengaluru, editing by Ed Osmond)
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