Woelki also used a seven-meter-long former refugee boat as his altar for the service to celebrate the Feast of Corpus Christi. The boat had previously been recovered by the Maltese military during a search-and-rescue operation.
The cardinal emphasized the significance of choosing the boat, saying that altars had always symbolized Jesus Christ. "To see those in need and help them is the task the Lord has given to us as Christians," said Woelki.
"Their cry for justice, for dignity and peace are also God's cry," the archbishop commented, according to a translation by Austria's Catholic Press Agency.
Self-critically, Woelki went on to suggest that those saying Islam was being abused as a religion should remember that Christianity had also cost people's lives in the past.
The symbolic gesture by one of Germany's most influential cardinals came the same day dozens of refugees were feared to have drowned while trying to reach European soil. It was at least the second boat to capsize within only two days.
Since Monday, about 7,000 refugees were rescued in different operations across the Mediterranean, according to officials.
Although fewer refugees have so far arrived in Europe via boat this year compared with 2015, the number of rescue missions recently increased because more migrants risked the dangerous journey due to improved weather conditions.
But those who survive the sea crossing will hardly experience a welcoming atmosphere in Europe. Whereas the continent was split last year on the question of whether to welcome refugees, even the most liberal countries are now remarkably skeptical of the influx. In Austria, Sweden and Germany — arguably the three most welcoming bigger nations in 2015 — right-wing parties are on the rise.
Austrians nearly elected a right-wing president on Sunday, which came as the latest warning sign to many liberal politicians across Europe.
In Germany, publicly voiced skepticism mainly emerged following incidents of mass rape on New Year's Eve in the city of Cologne. Dozens of male refugees and migrants were later accused of being mainly responsible for those assaults.
Amid tensions between supporters and opponents of migration, the Catholic Church has emerged as a crucial defender of refugees in Germany.
Last year, Woelki raised attention when churches rang their bells 23,000 times to commemorate the thousands believed to have died in the Mediterranean sea since 2000.
Since the beginning of 2014 alone, about 8,000 refugees are believed to have died after their boats sank or capsized, according to the International Organization for Migration.