Mr Barroso and Italian Prime Minister Enrico Letta were heckled by local residents shouting "Shame" when they arrived on Lampedusa, prompting them to make an unplanned stop at its badly overcrowded immigration centre.
Mr Barroso pledged £25 million in emergency funds that can be used to improve conditions at the immigration centre, where hundreds have been forced to sleep outside on the ground for days.
Mr Barroso and Mr Letta also paid their respects to the dead, standing before some 280 coffins arranged in rows. Some of them, small and white, held the corpses of children.
"The image of hundreds of coffins will never get out of my mind," a visibly shaken Mr Barroso said as Mr Letta announced a state funeral would be held for the victims.
The tragedy occurred when a fire broke out on board less than half a mile off Lampedusa, creating a panic that capsized the boat, according to testimony from some of the 155 survivors. They had set out from Libya, paying hundreds of dollars for the passage.
Divers recovered nine more bodies yesterday, bringing the confirmed dead to 297, the coastguard said. More than 300 are estimated to have perished.
EU Home Affairs Commissioner Cecilia Malmstrom also expressed shock at the sheer number of dead, saying: "This is not the EU we want. We need to do everything we can to prevent this from happening again. It requires EU action."
With Lampedusa just over 70 miles from Tunisia, Italy has borne the brunt of migration from North Africa for more than a decade.
As of a week ago, about 30,100 migrants had reached Italy by sea this year, according to UN refugee agency data. Of those, 7500 fled the Syrian civil war, 7500 political oppression in Eritrea and 3000 violence in Somalia.
Unlike in previous years, almost all the seaborne migrants could qualify for refugee status, in part as a result of the Arab Spring uprisings that led to political instability across the southern fringes of the Mediterranean.
Migrants began making the dangerous crossing from North Africa two decades ago, and the 20 sq km island has been a stepping stone for thousands seeking better lives in Europe ever since.
Mr Letta said: "Our presence here today is a way to tell all European states that this is a European problem."
Ms Malmstrom proposed at a meeting of EU interior ministers on Tuesday the idea of ramping up patrols across the Mediterranean to "save more lives" and backed a task force to better coordinate border control efforts.
But she also said there was "no political support" for the idea of having a central bureaucracy to divide up asylum seekers among the 28 member states. Seven EU states, including Germany and France, now take in almost all refugees, she said.
Italian EU Affairs Minister Enzo Moavero Milanesi has called for a far-reaching overhaul of Europe's immigration policies, saying the idea of reforming the asylum regulations "must not be a taboo".
Taking up an invitation from Lampedusa's fiery Mayor Giusi Nicolini, Mr Barroso, Mr Letta, Ms Malmstrom and Italian Interior Minister Angelino Alfano visited the immigration centre, whose conditions Mr Letta described as not worthy of a civilised country.
Almost 900 migrants are packed into a centre built for 250, prompting repeated protests in recent days from the UN's refugee agency.