Faith implies assent of the intellect to that which is believed. Now the intellect assents to a thing in two ways. First, through being moved to assent by its very object, which is known either by itself (as in the case of first principles, which are held by the habit of understanding), or through something else already known (as in the case of conclusions which are held by the habit of science). Secondly the intellect assents to something, not through being sufficiently moved to this assent by its proper object, but through an act of choice, whereby it turns voluntarily to one side rather than to the other: and if this be accompanied by doubt or fear of the opposite side, there will be opinion, while, if there be certainty and no fear of the other side, there will be faith.
Thus St. Thomas, like Cardinal Newman, clearly pits doubt against faith: When doubt persists, then all one has is opinion; whereas when authentic faith is present there is certainty.
Because science  is incompatible with opinion about the same object simply, for the reason that science demands that its object should be deemed impossible to be otherwise, whereas it is essential to opinion, that its object should be deemed possible to be otherwise. Yet that which is the object of faith, on account of the certainty of faith, is also deemed impossible to be otherwise; and the reason why science and faith cannot be about the same object and in the same respect is because the object of science is something seen whereas the object of faith is the unseen, as stated above.
Thus according to St. Thomas, science and faith are equally certain, the difference being that science is certain about things that it sees, whereas faith is certain about what is unseen (cf. Heb. 11:1): “Now those things are said to be seen which, of themselves, move the intellect or the senses to knowledge of them. Wherefore it is evident that neither faith nor opinion can be of things seen either by the senses or by the intellect.”
 “Science [in this context] is not taken in the restricted meaning of natural sciences, but in the general one given to the word by Aristotle and St. Thomas Aquinas. Aristotle defines science as a sure and evident knowledge obtained from demonstrations. This is identical with St. Thomas’s definition of science as the knowledge of things from their causes.” New Advent Catholic Encyclopedia, article on “Science and the Church”