"The northern command Major-General Udi Adam requested this morning to resign his position in the near future," an army statement said on Wednesday.
"The chief of staff has accepted Adam's request and he will be replaced in accordance with IDF [Israel Defence Forces] procedures."
Local media reports said Adam tendered his resignation because of differences with army chief of staff Dan Halutz over the conduct of the 34-day offensive on Hezbollah, which ended under a UN-brokered ceasefire on August 14.
Some Israeli military affairs commentators had questioned whether Adam, a tank officer, had been the right choice to head the Northern Command and lead a campaign that relied largely on air power, artillery and infantry.
Adam had been widely expected to leave the army in the wake of a decision near the end of the 34-day war to appoint another general as "co-ordinator of operations in Lebanon" at the Northern Command.
"The state of Israel definitely owes [Adam] a great debt," Amir Peretz, the defence minister, told Israel Radio.
Defence Minister Peretz (L) too
is under fire over his conduct
"No doubt we need to examine the meaning of the [move], why he decided to do it ... such an announcement by a general cannot be ignored."
On Adam's watch, Hezbollah seized two Israeli soldiers and killed eight other troops in a cross-border raid on July 12, an operation that triggered the fighting that ended in a ceasefire on August 14.
Hezbollah fired nearly 4,000 rockets into Israel, embarrassing the Middle East's most powerful army, and the soldiers are still being held.
Under public pressure, Ehud Olmert, the Israeli prime minister, on Monday appointed a retired judge to head an inquiry into the way the government and the military handled the war.