Cricket South Africa (CSA) had identified Amla, one-day skipper AB de Villiers and Twenty20 leader Faf du Plessis as the potential successors to Graeme Smith, who retired from the international game in March.
Having initially ruled himself out, Amla had a change of heart in recent weeks and will now lead the side to Sri Lanka for a two-match series next month.
Amla believes it is the right time for him to take over after the loss of senior players Smith and Jacques Kallis in the past six months.
"This is an exciting challenge but one that I take on with positivity with our test team being in an exceptionally good space at the moment with the support of a strong core of senior players," he said in a statement.
"I have concentrated on taking my batting to the highest possible level and now I feel I am in a position to make a contribution to South African cricket in a leadership role."
Amla's appointment is surprising only in that he has, by his own admission, shied away from leadership roles in the past.
De Villiers will keep the vice-captaincy position he filled under Smith, and will remain in charge of the ODI squad with Amla as his deputy.
The prospect of De Villiers giving up the wicketkeeper gloves to become captain would have upset the balance of the test side and is believed to have counted against him.
Amla's promotion comes after the South African government recently spoke of its desire for greater racial transformation within the game.
CSA chief executive Haroon Lorgat last month urged selectors not to fall back on an "automatic choice" for the captaincy, but to consider all options.
"Hashim is universally respected, both in South Africa and around the cricketing world, not only for his quality as a player, which has seen him ranked among the best batsmen in the world in both test and ODI cricket, but also for his personal qualities," Lorgat said in a statement.
"He has earned particular respect as a role model for his humility and his upholding of the best traditions and spirit of the game. Becoming captain is a natural progression for his outstanding career and we are indeed fortunate to have a leader of his quality."
Amla is the fifth player to be appointed captain of the Proteas since South Africa were readmitted to international cricket in 1992.
He follows Kepler Wessels (1992), Hansie Cronje (1994), Shaun Pollock (2000) and Smith (2003), although Mark Boucher, Kallis and Ashwell Prince have also done the job in a stand-in capacity.
Amla will take South Africa - who last month lost the number one test ranking to Australia - to Sri Lanka for a two-test series next month, and will also lead them in a five-day game in Zimbabwe and a home series against West Indies later this year.
(Reporting by Nick Said, editing by Stephen Wood)
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