They also chose Baroness Catherine Ashton, a Briton little known even in her own country, as EU foreign affairs chief under a deal that kept out more established figures such as Tony Blair, and raised questions about how the bloc plans to lift its profile.
The appointments are intended to bolster the EU's standing and help it to match the rise of emerging powers such as China following the global economic crisis, but neither Ashton nor Van Rompuy is a familiar figure outside Europe.
I believe my experience will speak for itself. Am I an ego on legs? No I'm not. Do I want to be seen to be out there saying everything all the time? No I don't. Judge me on what I do and I think you'll pleased with the outcome, Ashton told reporters.
Von Rompuy promised to move step by step to help Europe out of exceptionally difficult times, a period of anxiety, uncertainty and lack of confidence.
Van Rompuy, 62, and Ashton, 53, are compromise candidates who plan to use quiet diplomacy and consensus. At least initially they will not have the weight in foreign capitals that a better-known figure such as Blair, a former British prime minister, would have had.
Agreement on the positions took weeks, undermining efforts to present the bloc as a united force, partly because Britain had demanded Blair should be president.
The breakthrough came when Prime Minster Gordon Brown dropped that demand and backed EU Trade Commissioner Ashton as high representative for foreign affairs and vice-president of the EU's executive European Commission instead.
The presidency role was created under the EU's Lisbon reform treaty, which will make decision-making easier in the bloc and creates a diplomatic corps to be headed by Ashton. She replaces Spaniard Javier Solana.
EU leaders had sought a political balance to satisfy member states and the European Parliament, whose approval is needed for Ashton. This was achieved by appointing a center-right president and a center-left high representative for foreign affairs.
Van Rompuy, who will not need the assembly's approval, won plaudits for holding together Belgium's fragile coalition government after becoming prime minister less than a year ago.
Ashton, a former member of the House of Lords, Britain's upper house of parliament, has little foreign affairs experience. But she has made a good impression as trade commissioner.
I'm one of those people that believe that characters can grow into jobs, German Chancellor Angela Merkel said.
Blair had long been the front-runner but many other states wanted a candidate more likely to lead by consensus, and Germany and France joined forces to block his candidacy.
They remain powerful forces in the EU although they have none of the top jobs which also include a Portuguese, Jose Manuel Barroso, as European Commission President.Barroso will now complete the line-up of the Commission under him and Ashton. Deals are sure to have been made on some of the jobs during the consultations on the top jobs led by Sweden, which holds the EU presidency for the rest of this year.
EU diplomats said it was now all but certain that former French Foreign Minister Michel Barnier would be commissioner for the EU's internal market, one of the most powerful and most sought-after positions in Barroso's team.
Failure to agree on the top jobs would have highlighted divisions in a bloc representing nearly 500 million people, and undermined the goal of boosting the EU's image abroad.
In backing Ashton, the leaders also answered calls by many EU officials for a woman to have one of the Union's top posts.
(Writing by Timothy Heritage, editing by David Stamp)