US Secretary of State Hillary Clinton placed second, followed by Brazilian President Dilma Rousseff, making the top three spots unchanged from last year. Sonia Gandhi, president of the Indian National Congress, was at No. 6.
The list named women involved in policymaking, entertainment, technology and nonprofit organizations, among other fields. They were ranked according to influence, the amount of money they control or earn, and media presence.
"These power women exert influence in very different ways and to very different ends, and all with very different impacts on the global community," said Moira Forbes, president and publisher of ForbesWoman.
The magazine noted Merkel's resolve in preserving the European Union and her influence over the euro zone's ongoing debt crisis.
Ms Clinton was applauded for her handling of crises such as the release of a trove of diplomatic cables by the anti-secrecy group WikiLeaks.
Forbes cited Ms Rousseff for her leadership of the world's eighth-largest economy and approval ratings within her country.
The average age of the 100 power brokers from 28 countries was 55. They had a combined 90 million Twitter followers, Forbes said.
Also in the top five were Melinda Gates, co-chair of the Bill & Melinda Gates Foundation and wife of Microsoft Corp co-founder Bill Gates, and Jill Abramson, executive editor of the New York Times.
US First Lady Michelle Obama, who had topped the list in 2010, was No. 7.
The list featured newcomers such as actress and performer Jennifer Lopez and billionaire philanthropist and widow of Apple founder Steve Jobs, Laurene Powell Jobs.
Republican US Representative of Minnesota and former White House hopeful Michele Bachmann was among 21 women who fell off the list this year.
Christine Lagarde, managing director of the International Monetary Fund, was No. 8. The former French cabinet minister has been on the list since it began in 2004.
"So many of these women are in policy or political roles, and their influence ... is only growing so it's not surprising that someone like Merkel or Clinton would continue to be present on the list year to year," Forbes said.
The full list is at www.forbes.com/power-women.