In an unusually personal message, he said there had been "many days of sunshine" but also "times when the water was rough ... and the Lord seemed to sleep."
But even as the church passes through stormy seas, God will "not let her sink," he added, in what was his final general audience before he steps down Thursday evening.
Those words will be seen by many as a comment on the series of child sex abuse scandals and corruption claims that have rocked the Roman Catholic Church in the course of his pontificate.
Benedict recounted how when he was asked to be pope eight years ago, he had prayed for God's guidance and had felt his presence "every day" since.
"It was a part of the journey of the church that has had moments of joy and light, but also moments that were not easy," he said.
Meanwhile, the cardinals who must elect the new pope are already gathering in Rome, Lombardi said.
The dean cardinal will on Friday summon the cardinals to a general congregation, Lombardi said. That could come as soon as Monday, although the date is not yet fixed.
The cardinal-electors will then decide exactly when to hold the conclave, during which they will select a peer via paper ballot. The voting process will end when only when one cardinal gains two-thirds support.
After his resignation, Benedict, who cited the frailty of age as the reason he resigned, will no longer use the Fisherman's Ring, the symbol of the pope, Lombardi said. The ring will be destroyed, along with Benedict's papal seal, after his departure from office.