The foreign minister only took over the post in August and was the first to quit the cabinet since the Conservatives won power in January 2006.
Harper said that Bernier's controversial relationship with Julie Couillard was not a factor in the decision.
But, the resignation came as Bernier's former girlfriend was to appear on a French-language television station to say that her former lover was careless with classified papers.
The documents in question were left at a private residence earlier this spring, Harper said in a statement. He did not say what the documents were or if they were shared with others.
Bernier wrote in his letter of resignation that he asked the foreign affairs department to conduct a thorough review of the situation.
"Prime minister, the security breach that occured was my fault and my fault alone and I take full responsibility for my actions," Bernier wrote.
David Emerson, the international trade minister, is to replace Bernier temporarily.