I'm going to preface my post by letting the OP know that he has not asked a purely historical question. Capitalism and mercantilism are doctrines or theoretical approaches to economics. As such there always has been and always will be disagreements on what they actually are. In particular, mercantilism was not really defined in its time in any comprehensive way. The term mercantilism was not really even used by those we now call "mercantilist".

With that out of the way, I'm going to strongly disagree with the previous post by /u/mahelas here. The differences are not simple, generalization is not helpful, and most crucially capitalism and mercantilism are simply different things that cannot be directly compared.

"Capitalism" can be described as a fundamental economic structure defined by private ownership of property and the means of production, the profit motive as the driving economic impulse, and some form of competitive market competition. It does not mean utterly unregulated global free markets or no state participation in the economy at all. Many different state economic policies are possible in a capitalist economic system.

Mercantilism is not an economic structure in that sense. Rather it describes state economic policy that views international trade as a zero sum game and seeks to hoard bullion. It is primarily an approach to international economic relations, not the fundamental structure of the economy. In particular, it was as concerned with defense, imperialism, and colonialism as it was actually maximizing economic growth.

When viewed this way, mercantilism and capitalism are not opposed at all and did not clash. Historical mercantilism was capitalist. What clashed was mercantilist capitalism and laissez faire capitalism. You could have a mercantilist approach to state policy laid over a capitalist economic structure. But you could also (theoretically) have a mercantilist foreign policy laid over a centrally planned economy.

What I'm getting at here is this is mostly a question of definitions, and one that is not settled today. Many economists and historians view mercantilism as an early approach to capitalism.

For a couple different historical perspectives, to demonstrate how the idea of mercantilism has been handled over time.:

Wood's The Origin of Capitalism: A Longer View approaches this from a Marxist position and argues that trade systems have little to do with whether an economy is capitalist, because a trade system is separate from the means of production. In this sense, mercantilism describes the approach to trade and not ownership of production, and is therefore independent of capitalism. My description is horribly oversimplified, but generally Marxist definitions of capitalism have less to do with commerce and more to do with control of property and production.

The Liberal Elements in English Mercantilism by William D. Grampp was a landmark paper demonstrating that the gold hoarding mercantilist caricature was much more nuanced, and that actual mercantilist practice could often be quite concerned with maintaining healthy markets and investment.

The "Notes on Mercantilism" chapter of Keynes' The General Theory of Employment, Interest, and Money is a readable take on the relationship between mercantilism and modern economic theory.

Lastly, I'd actually suggest you read Adam Smith's works in order to get the contemporary perspective. The modern narrative places Smith diametrically opposed to mercantilism. Yet Smith supported some centerpieces of mercantilist policy, notably the Navigation Acts.