Susic's position was under question after his team were eliminated in the group stages of the FIFA World Cup.
Bosnia finished behind Argentina and Nigeria in Group F in a disappointing maiden World Cup campaign.
But the country's federation have decided to retain Susic for the next two years as they look to qualify for the European Championships for the first time.
"[The federation] decided that Safet Susic will remain coach of Bosnia-Herzegovina for the next two years," they said in a statement on Wednesday.
Susic told reporters: "I said that to leave the team would be painful for me. And that moment has not yet come
"I am really happy to be continuing."
Belgium, Israel, Wales, Cyprus and Andorra are in Bosnia's qualifying section for Euro 2016.
Susic will lead his team into their first Group B game on September 9, when they host Cyprus.
