Jalali announced his resignation on Tuesday in an interview broadcast on Afghanistan's private Tolo television channel.
"I will not stay in the interior ministry ... one main reason is that I have asked that I would like to resume my academic and scientific research," he said.
Jalali's departure will be seen as a blow for US-led international efforts to encourage the formation of a modern technocratic administration in Afghanistan after more 25 years of war and factional violence.
A Western-educated technocrat and a former soldier and journalist, Jalili returned to Afghanistan in 2002 after decades of exile in the United States, where he had headed the Afghan-language services of the Voice of America in Washington.
Officials and analysts have said he has been at odds with Karzai over the president's appointments to important provincial posts because of concerns that they would pursue factional interests.
Jalali has also openly complained that some government officials are involved in Afghanistan's massive narcotics trade, which analysts describe as the biggest obstacle to the country's long-term security.
Analysts also say he has been unhappy about a constitutional requirement, barring ministers from holding dual citizenship, that would oblige him to give up his American passport.
Jalali claims that government
officials are involved in narcotics
Government spokesman Karim Rahimi said he had no information about the resignation, but told a regular news conference: "Everyone has the right to resign or to work."
Khaliq Ahmad, an official at Karzai's presidential palace, said he had heard from local media that Jalali was planning to resign, but said he had not tendered his resignation to Karzai.
Rumours swirled earlier this year that Jalali had threatened to resign, but had been persuaded to stay by Karzai.
Jalali's move follows elections for a national assembly and provincial councils held on 18 September, the results of which will not be revealed until October.
Some analysts had expected him to wait for the formation of the parliament before resigning.