Justin Welby said he was left asking why the attacks happened, and where God was in the French victims' time of need.
He said he reacted with "profound sadness" at the events, particularly because he and his wife had lived in Paris.
Asked if these attacks had caused him to doubt where God is, he said: "Oh gosh, yes," and admitted it put a "chink in his armour."
He told BBC Songs Of Praise: "Yes. Saturday morning - I was out and as I was walking I was praying and saying: 'God why - why is this happening? Where are you in all this?' and then engaging and talking to God. Yes, I doubt."
When asked what his reaction to the attacks was, he said: "Like everyone else - first shock and horror and then a profound sadness - and in my family's case, that is added to because my wife and I lived in Paris for five years.
"It was one of the happiest places we have lived and to think of a place of such celebration of life seeing such suffering is utterly heart-breaking."
A bombing campaign against Islamic State was launched after the events, but the Archbishop warned against a potentially damaging instant reaction.
"Two injustices do not make justice," he said. "If we start randomly killing those who have not done wrong, that is not going to provide solutions. So governments have to be the means of justice.
"The Bible tells us that they are put there by God with the sword for justice, but they also have to lead us into a place where peace can be established."
The Archbishop said the way Islamic State terrorists had distorted their faith to the extent they believe they are glorifying their God is "one of the most desperate aspects of our world today."
"Religion is so powerful in the way humans behave that it has always been a tool used by the wicked to twist people into doing what they want them to do.
"But just because someone believes something deeply wrong does not mean that they are right in some way because they put God in it. The perversion of faith is one of the most desperate aspects of our world today."