The Red Rose skipper has not played since last month's Six Nations defeat to Ireland at Twickenham.
Hartley, 32, said: “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.
“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.
“I intend to use this time to recover fully from my injury, so I can be ready to hit the ground running when pre-season training starts later this summer.”
The news over 93-capped Hartley is a blow for Eddie Jones' ahead of the Three Test Springbok tour in June.
After missing 14 weeks of the 2015/16 season due to bangs to his brain Hartley admitted it might be the end of his professional playing career if he suffered another.
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Just a day after lifting the 2016 Six Nations Grand Slam he exclusively revealed to SunSport that he couldn't even remember picking up the silverware and doing a lap of honour.
He only just managed to shake off the symptoms to lead England to a historic series whitewash over Australia.
Back then, he said: “If I got another one now, I would be worried.
“I would probably start looking at other careers or stuff like that, or maybe a long lay-off. Maybe I need to look at my tackling technique, too.
"I just had a constant reminder every time that you see your kid and you think: ‘If I hit my head again, what’s that going to mean?'"
Speaking about the battle to get back fit, Hartley said: “I thought, ‘right, it’s been a month now and I’ve done absolutely f-all, I’m going to go and get on my Watt bike’.
“I put all my kit on, put my water bottle on – and I just couldn’t get on the bike. I had no urge to get on the bike.
"I almost tried forcing myself to get on the bike and I just said: ‘I can’t be bothered’, went back to lie on the coach and went to sleep. Then I knew that I wasn’t right.”
In Hartley's absence Saracens fly-half Owen Farrell will skipper England – but that's only if boss Jones makes a u-turn on his decision to rest his Lions stars.
England have already been crippled with injuries in a huge blow to their Japan 2019 World Cup preparations.
Hooker Hartley joins Anthony Watson, Jonathan Joseph, Courtney Lawes and Nathan Hughes on the sidelines.
But Hartley has still be involved in meet-ups with Jones and the rest of the England leadership team before they head off this summer.
His international back-up, Jamie George was a Lions starter, so Jones can not afford to rest him now either.
And the Aussie boss will most-likely bring in Exeter Chiefs' Luke Cowan-Dickie as the back-up when he names his squad on May 10 to travel to the Southern Hesmisphere.
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