The synod is the ruling body of the Church of England
The Church of England's ruling council has passed a motion calling on Church leaders to emphasise the compatibility of belief in both God and science.
The motion urges the Church to fight back in what is the latest move in a battle between atheists and believers.
The motion at the general synod in London was proposed by Dr Peter Capon.
He believes atheists are forcing the public to choose either belief in God or the logic of science in a bid to push religion out of the public sphere.
Critics say the two disciplines contradict each other, and accuse religious groups of seeking to hamper and reverse scientific breakthroughs.
The motion was passed 241 to two, with two abstentions.
John McManus, religious affairs producer, BBC News
Dr Peter Capon proposed his motion because he wants the Church to make a stand against well-known atheists, such as Prof Richard Dawkins, who say that science has disproved God's existence, and therefore it doesn't make sense to believe in both.
Prof Dawkins has riled many in the religious world and his name was mentioned throughout the debate, along with a fair smattering of scientific theories.
But Dr Capon's motion was never going to be just about whether religion trumps science, or vice versa.
Instead, he was making a plea for faith to be allowed to have its own space apart from science, equal but different.
Though he admitted that many of the universe's mysteries had been solved by rational enquiry, he and many other speakers repeated their belief that some aspects of existence couldn't be explained by the people in lab coats.
And that is where the two sides will never agree.
Dr Capon's motion has come in response to what many in the Church perceive as a growing pressure on the public to choose between the merits of either religion or science.
A former lecturer in computer science, Dr Capon said atheists were misleading the public when they claimed science and religion are incompatible.
He believed that some popular science and nature programmes also repeated this line too easily, ignoring the fact that many scientists hold spiritual beliefs.
Dr Capon said he wanted "to refute the crude caricature of faith, as being blind and irrational, propagated by some atheist scientists".
He told the synod he rejected the notion that "science can resolve all questions capable of being answered", arguing that questions about the existence of God and the meaning of life were "quite beyond scientific explanation".
The Bishop of Southwark, the Right Reverend Dr Tom Butler, said "the average person's view is that science has disproved religion".
But he spoke of the scientific theory of dark matter, which he said involved "a lot of dark matter which we can't even see, being propelled by forces we don't understand".
He added: "And they say that religion is all about faith."
Another delegate, Philip Brown of Manchester, said: "Science can only explain how something was created; religion can explain why."
Gavin Oldman, of Tring, Hertfordshire, told the synod that he had trained as an engineer and that logic drove his faith as well.
He added that gravity, light and time were all manifestations of God's love.
The synod meets twice-yearly to discuss issues relating to the running of the national Church.
Delegates have also been hearing how the Church plans to implement the introduction of female bishops.
Additionally, it has voted to back a motion expressing "deep concern" at what it believes is a cut in religious TV programming.