"I remain confident in President Karzai's leadership and his ability to appoint credible replacements to lead these critical organizations charged with protecting the Afghan people and ensuring their sovereignty," McChrystal said in a press release after the meeting.
Earlier in the day, in a hastily arranged news conference, Saleh said there were "tens" of reasons why he was leaving his position, but would only admit that he had failed the president during the jirga.
"I want to thank colleagues who, for the last six-and-a-half years, always made sure the three color flag of Afghanistan flew high, safe from the threats of its enemies: al Qaeda and Pakistan," Saleh told journalists.
Pakistan, where many senior Taliban officials live, has long mistrusted Saleh. Senior Pakistani military officials have complained to ABC News about the Afghan FBI, known as the National Directorate of Security, or NDS, saying senior officials were giving Pakistan a bad name.
Just two weeks ago, Saleh accused Pakistan's premiere spy agency, the Inter-Services Directorate, or ISI, of training a suicide bomber who killed four Western colonels in Kabul in May.