Judges grant prosecution permission two days before Bujumbura's withdrawal.
The International Criminal Court (ICC) has granted chief prosecutor Fatou Bensouda's request to open war crimes investigation in Burundi.
The country plunged into a political crisis in April 2015 when President Pierre Nkurunziza decided to run for a third term, which he won in a disputed July election that year that was boycotted by the opposition. His opponents said it was unconstitutional.
According to UN and human rights bodies, between 500 and 2,000 people have since been killed in clashes with more than 400,000 people having fled and dozens of opposition activists forced into exile.
In a statement Thursday, the court said it allowed the probe on October 25, two days before Burundi formally withdrew from the Rome Statute that established the ICC.
The court said it still has jurisdiction over alleged crimes committed while the country was a member.
The judges found that there was "a reasonable basis to proceed with an investigation in relation to crimes against humanity, including murder, imprisonment or severe deprivation of liberty, torture, rape, enforced disappearance and persecution, allegedly committed in Burundi, and in certain instances outside of the country by nationals of Burundi."
The court said Bensouda can probe the alleged crimes since April 26, 2015 to October 26, 2017 but can also extend before and after that date "if certain legal requirements are met".
In a swift reaction, Burundi presidential office spokesman Willy Nyamitwe denounced the "corrupt" ICC in a tweet.
He accused the court of cheating and said it had just "shot itself in the foot."
"Without any doubt, Burundi will emerge the winner of this battle," he added.
-Additional reporting by AFP.