The math professor told guests at the Bible Society-sponsored event that atheism was a "delusion" and a "fairy tale for those afraid of the light".
He urged Christians to have "the courage to create public space" for the discussion of "a biblical worldview", as he pointed to the example of Tyndale, who translated the Bible into English 400 years ago and would eventually be executed.
Dr Lennox, who has been an outspoken critic of "God Delusion" author Richard Dawkins, blamed new atheism for the "moral drift" in society.
He also dismissed the common assumption that science and religion are not compatible.
"There is no necessary conflict between science and God, the real conflict is between worldviews, atheism and theism," he said.
"God is not the same kind of explanation as science is. God is the explanation of why there is a universe at all in which science can be done."
Dr Lennox admitted his fear that the contribution of Christianity to the moral foundations of British society would be forgotten in the prevailing climate. This could be seen already, he suggested, in the parliamentary expenses scandal and the Leveson inquiry.
"The playing field is not level since atheism has become so dominant … and is often regarded as the default position in the media," he said.
"If we teach people that morality is an illusion, they will begin to believe it. Many already have with the result that our institutions are awash with scandal, families are increasingly fractured, people are lonelier than ever and trust is at an all-time low. We have sown a wind and are reaping a whirlwind."
On the same day as the National Prayer Breakfast, Prime Minister David Cameron issued a statement affirming the place of Christianity in Britain.
"It is encouraging that Christianity still plays such a vital role in our national life. We are a country with a Christian heritage and we should not be afraid to say so," he said.
Prof Lennox responded, "No one in this country seems to have a problem with doing atheism in public. Let us not be ashamed of doing God."
Guests at the National Prayer Breakfast included MPs Fiona Bruce, Gary Streeter and Tim Farron.
Matthew van Duyvenbode, Head of Campaigns, Advocacy and Media at Bible Society said, "In a society searching for deeper meaning, a compelling witness to hope is required. Within the Scriptures, we find a tantalising vision of hope – one which stimulates, provokes and invites us to become the signs of hope for others."