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"This has been a difficult affair that I would gladly have done without," Prime Minister Erna Solberg told a joint press conference.
"I am honestly saddened that things have come to this. We will miss his contribution to the government."
Wara, 53, had taken temporary leave from his position a fortnight ago after it emerged that the Norwegian security service PST was investigating his partner, Laila Anita Bertheussen.
She was formally named a suspect on Thursday.
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"The past few weeks have been hard on me and my family. The decision (to resign) was entirely my own," said Wara, of the right-wing populist Progress Party and who had held the job just under a year.
In late 2018, Bertheussen filed a complaint against a theatre troupe for showing pictures of the homes of several politicians -- including theirs -- as part of a play aimed at demonstrating who was profiting from a more segregated and racist Norway.
After that a series of attacks began against the couple.
Among other things, the couple's home was vandalised in December 2018 when a swastika and the word "racist" were drawn on their house and car, and their car was set ablaze outside their home in mid-March.
In an op-ed piece written in daily Verdens Gang, Bertheussen claimed the production was an invasion of her privacy.
Solberg had also criticised the theatre troupe.
Wara's party colleague Jon Georg Dale will take over as interim justice minister until a permanent replacement is appointed.