Jamil al-Sayyid, head of General Security, sent a letter of resignation on Monday, in which he wrote: "Security chiefs are usually appointed according to politics and change with political changes."
He said he was resigning to avoid confusion and because of a change in policy in Lebanon dictated by the changing political developments.
"I am honoured to request that my services be terminated and that the resignation is accepted," he said in his statement.
Al-Sayyid's resignation had not been expected so soon, Aljazeera's correspondent in Beirut, Ghassan bin Jiddo, said.
Speaking to Aljazeera in Beirut, outgoing Lebanese minister Karam Karam said the assassination of former prime minister Rafiq al-Hariri and the UN-sponsored fact-finding team's report into the killing, had made the security service chiefs' resignations inevitable.
Karam said the heads of the security services had to submit their resignations, or else the cabinet would have had to sack them.
He said their departure was one of the main opposition demands in addition to being one of the unanimous demands of the Lebanese people, adding that the investigation into al-Hariri's killing could not proceed without their resignations.
"Security chiefs are usually appointed
according to politics
and change with
Interior Ministry's General Security Department
According to Aljazeera's bin Jiddo, pressure from the Lebanese Interior Ministry may have also played a role in al-Sayyid's resignation.
The interior minister had made unfavourable comments about the security chief in connection with the UN report into former prime minister Rafiq al-Hariri's assassination, causing al-Sayyid to quit in a hurry, bin Jiddo said.
Al-Sayyid, an army general, was director-general of the interior ministry's general security department, which handles passports, border controls and censorship of publications.
Moved to the ministry after President Emile Lahud was elected by parliament in 1998, al-Sayyid quickly became Syria's closest ally in the Lebanese security services.
Al-Sayyid had said last week he was ready to step aside during a UN-ordered international investigation into the 14 February assassination of al-Hariri.
The anti-Syrian opposition had demanded the resignation of the country's security chiefs after al-Hariri's death.