The finance ministry confirmed that a deal had been struck "solving the problem of the unpaid wages" and that Eini has agreed to several of the government's proposals.
Around 400,000 public workers went on strike at 9am (07:00 GMT) on Wednesday after all-night reconciliation efforts between the government and the Histadrut labour federation failed to resolve the row.
The strike had a crippling effect on airports, seaports, railways, government offices and many other essential services.
The union originally planned to start the strike at 6am (04:00 GMT) but delayed it to allow more time for negotiations with the government. The two sides had talked through the night.
An adviser to Ehud Olmert, the Israeli prime minister, began negotiations with Eini late on Tuesday in an attempt to avert the strike.