The motion, put forward by former computer science lecturer Dr Peter Capon, also urges the House of Bishops to take steps to improve public understanding of the compatibility of science and Christianity.
Dr Capon said he had put the motion forward in order to refute the "crude caricature of faith" as something "blind and irrational" being propagated by atheist scientists like God Delusion author Richard Dawkins.
He rejected the notion that science could answer all questions about existence, saying it was possible to see the meaning of life through science and through faith.
It was not only atheists to face criticism, however. Dr Capon said some Christians had embraced theories "for which there is scant scientific evidence", as he warned Christians would make a "categoric mistake" if they attempted to read the Bible as a modern scientific textbook.
He pointed to the growing popularity of young earth creationism in the US, which he accused of trying to "force a wooden literalism on the Bible".
"This so-called 'creation science' attracts conflict because it contradicts so much modern scientific understanding. Rejecting much mainstream science does nothing to support those Christians who are scientists in their vocation or strengthen the Christian voice in the scientific area. Nor does it help the Christian who is a science student in school, college or university or encourage their faith in a great Creator," he argued.
Instead, Dr Capon urged Christians to take scientific evidence seriously and avoid prejudging science for theological reasons.
The Bishop of Southwark, the Rt Rev Tom Butler, addressed Synod for the last time before he retires next month.
Supporting the motion, he said the disputes between science and religion were "unnecessary" and had only undermined the authority of the Church.
He said even believing in quantum physics, which relates to the behaviour and movement of invisible atomic and subatomic particles, required faith.
"If believing that isn't faith I don't know what is and I don't think that we need to be defensive about ours," he said.
"The new physics tells us then that we have on our hands a world of possibility and potentiality, a world which can be probed, provided we set aside our everyday perceptions."
The motion was passed 241 to two, with two abstentions.