Karis, a biologist and former director of the Estonian National Museum, won the support of 72 of the 101 lawmakers in the small Baltic nation's parliament, the Riigikogu.
He replaces current President Kersti Kaljulaid, with his inauguration scheduled for 11 October.
The president of Estonia is a largely ceremonial role and involves mainly representative duties.
Karis, 63, was the sole candidate for the role.
In the first round of voting on Monday, he was unable to gain the required two-thirds of the members of parliament needed to confirm.
The outgoing President of Estonia, Kersti Kaljulaid. Photo: Twitter/@KerstiKaljulaid.