In this statement, Aquinas is saying that mystery is not here to take out of the knowledge of nature, but mystery is around to perfect nature. The things revealed to human beings by divine revelation and faith do not negate science. In fact, nature works with faith in order to produce understanding to human beings.
When philosophy and faith come together into a solid understanding, they do not mix with each other allowing the message to be diluted. Instead, there is a transcendence of understanding into a new level of understanding different from faith and also different from philosophy.