More than 4 million Venezuelans have fled in recent years amid widespread shortages of food and medicine in their homeland.
Colombia has borne the burnt of the exodus - it is now home to more than 1.4 million Venezuelans, many of whom arrived with little money and in need of services like healthcare.
"I'm pleased to announce new help of 30 million euros for the identification of migrants and their socio-economic integration," Mogherini said during a joint Bogota press conference with President Ivan Duque.
"We support these efforts by the government and local authorities to offer employment, entrepreneurship and dignified housing for refugees, migrants, returned people and also receiver communities."
The EU has already given some 130 million euros to countries in the region to help them provide for migrants, Mogherini said.
Colombia and the EU will hold a conference in Brussels in October about the crisis, Duque said, in a bid to raise more funds for migrant care.
Colombia has repeatedly lamented a lack of funding for Venezuelans, saying other humanitarian crises in Syria, South Sudan and Myanmar have received many times more in donations from the international community.
The United States said last week it would give an additional $120 million in humanitarian assistance to help Latin America cope with the crisis.
Unlike its neighbors, Colombia has not imposed stringent immigration requirements on Venezuelans, instead encouraging migrants who entered the country informally to register with authorities so they can access social services.
Last month Duque announced Colombia would give citizenship to more than 24,000 children born in the country to Venezuelan parents, to prevent them from being stateless.