"All diplomatic, economic, financial measures and others are applicable from today and will not be lifted until the re-establishment of constitutional order," said the chairman of the 15-nation regional bloc, Côte d'Ivoire President Alassane Ouattara.
Non-Ecowas members Mauritania and Algeria, which border Mali to the north and west, were at the emergency summit in Dakar on Monday and will also implement the embargo.
The bloc will also put in place a military standby force, after earlier putting some 2,000 regional troops on alert, Ouattara said, calling the situation in Mali "extremely serious."
The vast landlocked country depends heavily on the import of fuel and basic goods from surrounding nations and the embargo will also cut the junta off from the regional central bank in Dakar, affecting its ability to pay public wages.
As Mali slid further into chaos under military rulers who seized power on 22 March, France called for an emergency meeting of the United Nations Security Council. But Paris said there was "no question" of sending troops and expressed concern over the role of Islamist groups in the rebellion.
On Monday, witnesses reported that Islamist fighters chased the Tuareg rebels out of Timbuktu, one day after both groups swept into the fabled city.
Though they have been fighting side by side over the past several months, the two groups have very different objectives.
Meanwhile, some 200,000 people have fled fighting in Mali, where widespread looting in key northern towns have also forced the UN food agency to suspend its activities.