In a dry, lecture-like address to the Bundestag, the pope touched upon the philosophical concepts of justice, reason and human nature. But he said Europe risked placing too much faith in scientific reason and positivism at the expense of its Christian cultural roots.
“All other views and values of our culture are relegated to a subculture, thereby giving Europe a status of being without culture compared to other cultures of the world at a time when it's challenged by extremist and radical elements,” the German pontiff said, apparently referring to Islamic extremism.
The pope also defended the role of nature and God in shaping Europe's cultural and political foundations, warning that a modern trend toward positivism, which he defined as the rule of logic and the rejection of metaphysics, threatened man's very humanity.
"To serve right, and to fight against the dominion of wrong is, and remains the fundamental task of the politician," he said.
The pope, 84, who had to be guided to the podium, also praised the emergence of the ecological movement in his native Germany,
He said it, "continues to be a cry for fresh air which must not be ignored or pushed aside just because too much of it is seen to be irrational."
"Young people (have) come to realise that something is wrong in our relationship with nature ... but that the earth has a dignity of its own and that we must follow its directives," he added.
His praise for environmentalism managed to get a few chuckles from MPs, as he joked he was not speaking out for the Green party.
“It's clear I'm not making propaganda for any specific political party here,” he said to laughs.
“We must listen to nature and answer accordingly.”
The speech, which wrapped up with a standing ovation from lawmakers, came amid strong criticism by leaders of the Greens and other left-leaning parties, which said his invitation threatened to undermine the separation of church and state.
Dozens of parliamentarians boycotted the address, with some seats filled by retired lawmakers to avoid too many being left empty.
However, much of the socialist Left party's section as well as the back benches of the Greens and the Social Democrats remained abandoned, the blue seats a clear indication of their absence.
At a protest nearby that drew a few thousand people behind police barricades, a Social Democratic member of parliament, Rolf Schwanitz, said he was skipping the speech because it made no sense "to invite the head of a dwarf state (the Vatican) to speak before the Bundestag."
In the 20-minute address, the pontiff avoided the hot-button issues targeted by his critics such as recent sexual abuse scandals and his fervent opposition to abortion, homosexuality and a bigger role for women in the Church.
Some 30 foreign dignitaries have addressed the Bundestag to date, including former US presidents Richard Nixon and George W. Bush, as well as current Russian Prime Minister Vladimir Putin while he was president.