In a sign that the bloc wants to move on swiftly, EU chiefs told Britain in a strongly-worded joint statement to "give effect to this decision of the British people as soon as possible, however painful that process may be."
The uncompromising stance came after Prime Minister David Cameron said he would resign and leave the negotiations for Britain 's departure from the 28-nation club to a successor who will be named by October.
Juncker, a former Luxembourg premier and strong federalist, said "no" when asked if the vote spelled the beginning of the end for a European Union that faces a huge rise in populist and eurosceptic parties.
- 'A wake-up call' -
Worried European leaders will hold a series of crisis talks in coming days, with Merkel saying she would host the leaders of France and Italy along with EU President Donald Tusk in Berlin on Monday to try to chart a reform plan.
"We take note of the British people's decision with regret. There is no doubt that this is a blow to Europe and to the European unification process," Merkel told reporters in Berlin.
With global markets in turmoil, she said it was important to "not draw quick and simple conclusions from the referendum in Great Britain , which would only further divide Europe."
Hollande said the Brexit vote was a "grave test for Europe," adding that the bloc "must show solidity and strength in its response to the economic and financial risks."
Italian Prime Minister Matteo Renzi echoed calls for reform, saying "Europe is our house" and that "the house needs to be renovated, perhaps freshened up".
Greek Prime Minister Alexis Tsipras, whose debt-hit country went through a referendum on its way to a bitterly-fought debt bailout, said the result could be a "wake-up call" for the EU to "change its policies".
But he warned that it could also be "the start of a dangerous path backwards for our peoples."
EU chief and former Polish premier Tusk -- who had earlier warned that a Leave vote could "end Western political civilization" -- put on a brave face, saying that "what does not kill you makes you stronger".
He insisted that the bloc was "determined to keep our unity at 27" and said the remaining leaders would meet separately without Cameron on the sidelines of a summit of the full 28 in Brussels next week.