Mtawarira, nicknamed 'The Beast', travelled with the Springboks squad from Dublin to Edinburgh on Sunday ahead of Saturday's EMC Test with Scotland, but will now return home.
Springbok coach Heyneke Meyer said on the South African rugby's website: "We've consulted with Beast and his cardiologist in Durban and although it's safe for him to play, we decided it would be best for him to return home and rest.
"The player's welfare is the most important consideration at this stage."
The 27-year-old, who has 41 caps, had an irregular heart rhythm, a hereditary condition, according to South Africa team doctor Craig Roberts.
Roberts said: "He has had this several times before and it's always been managed accordingly.
"This condition is not life threatening, but needs to be managed properly which is why we thought it would be in Beast's best interest to return to South Africa.
"He needs to have a repeat of the minor procedure he had in Cape Town earlier this year and it's important to notice that he is not at risk by playing with it, and his career is not in jeopardy."
A decision on a replacement will be taken in due course, with the Test at Murrayfield and against England to come.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
A cool looking all black rugby cleat with the high performance adidas is known for. Get in the Gear!
Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
The All Blacks Performance t-shirt is black with hints of blue from the training jersey. Very Cool.
The New Zealand All Blacks training jersey for 2013/14. Get in the Gear!
The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.