Shakir was given a caretaker role after Zico resigned in late November and has been rewarded for his impressive spell in charge of the Under-19 side.
The 49-year-old will have his hands full.
Iraq, currently 92nd in FIFA's latest world rankings published this week, is still in the running to qualify for the World Cup in Brazil and is third in Group B of the Asia Zone final qualifiers with five points from five games.
It is trailing second-placed Australia only on goal difference.
The top two teams qualify directly for the finals while the third-placed team goes into a play-off system.
However, Shakir's first task will be the Gulf Cup 2013 starting in Bahrain next week.