Cricket South Africa selection convenor Joubert Strydom says all-rounder Jacques Kallis remains "a cornerstone of the Test and one-day side".
Kallis resigned the vice-captaincy after being omitted from the squad to play in the inaugural ICC World Twenty20 on home soil in September.
CSA issued a statement on Tuesday registering its disappointment.
But Strydom said philosophically: "I was a bit surprised (by the resignation) but Jacques must do what he must do."
Speaking to iol.co.za, Joubert went on: "I spoke to him personally before we announced the team and he was very good to me.
"He told me he respected the decision, but that he would have to reconsider his position in general and how long he still wanted to play.
"There are long-term strategic decisions that I have to take. We have 11 Test and 11 one-day matches coming up in the next 18 months.
"Jacques is the cornerstone of our Test and one-day teams. We felt that because of what he brings to the Test and one-day teams, it wasn't worthwhile sacrificing him in the Twenty20."
CSA chief executive Gerard Majola had earlier taken a dimmer view of Kallis.
He said in a statement: "It is most disappointing that Jacques took a unilateral decision after speaking to me to publicly announce his resignation as vice-captain.
"This is regrettable.
"Jacques is employed by CSA, and we expected him at least to sit down at a meeting and go through the matter before he made his own decision to make a public announcement."