The payment crisis sparked a severe public dispute between Fatah and Hamas, just days after the establishment of the new technocratic unity government. Hamas claimed that the Palestinian Authority and Palestinian President Mahmoud Abbas should pay the salaries, while the PA rejected the demand.
Hamas senior official Moussa Abu Marzouk announced Monday that the workers would be given their salaries in the coming days.
Jihad al-Wazir, head of the Palestinian Monetary Authority, the Palestinians' central bank, said "All automatic telling machines at bank branches in the Gaza Strip are working again today."
Hamas forces withdrew from outside banks, where they had been preventing the use of ATMs.
All banking services would be available on Thursday morning, Wazir said.
Hamas demanded Thursday that the Palestinian Authority take employees of the disbanded Gaza government onto its payroll, after the PA's Gaza-based staff received their salaries but their Hamas counterparts went empty-handed.
After scuffles broke out at ATMs, Hamas security forces closed the banks.
The row over pay was the first hitch in a reconciliation deal between Hamas and the Palestine Liberation Organization that began with the formation of a new unity government.
The PA has so far refused to pay Hamas's 50,000 civil servants, who are not registered as its employees because they were appointed after the Islamist movement ousted bitter rivals Fatah - which dominates the PLO - from Gaza in 2007.
Although Hamas allowed banks to reopen Wednesday, it continued to levy financial pressure by confiscating a number of card machines from Gaza shops and supermarkets so customers could not pay by credit card.
AFP contributed to this report