The 23-year-old has been out of action since suffering a stress fracture in the RBS 6 Nations defeat to Wales, which capped an injury-hit tournament for the second row, after a knee injury caused him to miss England's opening two fixtures.
And Saints coach Jim Mallinder says the second row, who has 14 caps to his name, will not play a part in Northampton's Aviva Premiership title tilt nor England's three-Test trip to face the Springboks.
He told BBC Northampton: "We were hoping he might play some part this season but it's looking like he has not quite recovered enough from his shin injury, so it looks like he'll probably not play for the remainder of this season for Saints or for England.
"He is gutted, you want to be involved in the big games, that means semi-finals, if we get there, and finals and, of course, going on England tours.
"He has been a bit unfortunate, but what he has got to do is have a good off-season, make sure his body fully recovers, then train hard for us in pre-season and I am sure actually then he will come back fighting fit.
"He has got a lot of years to go has Courtney and we've got to look after him."
Lawes' Northampton team-mate Tom Wood had already been ruled out of the trip to South Africa after a recurrence of the foot injury that forced him to miss the Six Nations.
Leicester flanker Tom Croft will also miss out after suffering a neck injury in the Tigers' recent Premiership win at Harlequins.
One man who will be going to South Africa is Mike Catt, after the former England centre was yesterday added to boss Stuart Lancaster's coaching staff for the tour.
Catt, who will leave current club London Irish after Saturday's Premiership finale against Gloucester, has a chance to stake a claim for a full-time position having been awarded a deal until the end of June.
Former New Zealand coach Wayne Smith was seen as the leading candidate for the role of backs coach, but, despite being impressed by Lancaster's vision for England's future, he chose to remain with Super 15 side the Chiefs due to family reasons.
And Catt, seen by many as one of the sharpest rugby minds in the British game, sees no reason why Lancaster should not be able to tap into Smith's knowledge, despite the Kiwi turning down a role with England.
Catt, who won 75 England caps as a player and was part of the World Cup-winning squad of 2003, said: "I still don't know why Stuart can't tap into Wayne's knowledge anyway.
"Graham Henry is still doing stuff around the world and I think Stuart has a good enough relationship with Wayne to be able to do that.
"I think everyone could learn massively from Wayne, but obviously for family reasons he's decided not to get involved but it gives other people opportunities to stake their claim.
"This is my opportunity. My focus is on the now.
"I had quite a few of them for England as a player and now this is my opportunity as a coach to make sure I can set my stall out and work well with Graham (Rowntree) and Stuart and the players."
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