The Northampton captain has been unavailable since sustaining the injury in the final match of the NatWest Six Nations against Ireland at Twickenham on 17 March, missing three rounds of the Aviva Premiership.
Concerns were raised over his absence in light of the concussion record that prompted an admission in 2016 that another significant blow would force him to reconsider his future in the game, and he has now been stood down until pre-season for the 2018-19 campaign.
“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. “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.”
Two years ago, 32-year-old Hartley, pictured, was ruled out for a total of 14 weeks due to two separate concussions, the last in the Grand Slam-clinching victory over France in which he was knocked out.
The hooker later conceded he had no memory of the trophy presentation and questioned whether another substantial head knock could result in his early retirement. He has been ever-present as captain under coach Eddie Jones but the Australian must now turn elsewhere for the three-Test series against the Springboks that takes place in June.
Owen Farrell is the front-runner as the Saracens playmaker was placed in charge when Hartley missed the March showdown with France because of a tight calf.
However, Jones had indicated he might look to rest some of his British and Irish Lions with next year’s World Cup in mind. Maro Itoje is another possibility but he falls into the same Lions category as Farrell, thinning the options to George Ford and Chris Robshaw.
The growing number of absentees from South Africa, however, may force Jones to abandon his plan to give some of the players involved against New Zealand 12 months earlier the summer off.
Jonathan Joseph (ankle), Anthony Watson (Achilles), Nathan Hughes and Courtney Lawes (both knee) will play no part, while Billy Vunipola has not played since January because of a broken arm.
Jamie George is the obvious choice to deputise at hooker as Hartley watches the tour from home.