"Pope John Paul II's passing is a sad event for the entire international community. His voice has for decades been a clarion call for global peace and justice," de Hoop Scheffer said in a statement.
The 84-year-old spiritual leader of the Roman Catholic Church's 1.1 billion members passed away at 9:37 pm (1937 GMT) Saturday, after suffering two days of heart and kidney failure and two months of acute breathing problems and other ailments.
"Through his personal determination and courage, he played a pivotal role in bringing democracy and freedom to millions of people in Central and Eastern Europe," de Hoop Scheffer said.
"He will certainly leave a legacy as one of the historic figures of the 20th century."
Expressions of grief and admiration from around the world have highlighted John Paul II's role in the downfall of communism and his message of peace.
The pope lent his immense prestige to the outlawed Polish trade union Solidarity and triggered a chain reaction that led to the fall of the pro-Soviet regimes which had held half the continent in thrall for 40 years.