One should keep in mind two points. First, historical materialism in its traditional form is later Marx, taking final shape in Das Kapital, the theory of alienation is young Hegelian Marx of 1844 Manuscripts, and the "species-essence" is borrowed from his left Hegelian predecessor, Feuerbach. In 1845 Theses On Feuerbach Marx reinterprets him in the general spirit of "demythologizing" the Hegelian Geist:"Feuerbach resolves the religious essence into the human essence. But the human essence is no abstraction inherent in each single individual. In its reality it is the ensemble of the social relations". Compare to Critique of Hegel’s Philosophy of Right: "Precisely because Hegel starts from the predicates of universal determination instead of from the real subject, and because there must be a bearer of this determination, the mystical idea [Geist] becomes this bearer". The alienation theory of young Marx was developed by Lukac in 1920s.
Second, even late Marx is not a plain materialist but a dialectical materialist, and, as Hegel wrote and Marx emphatically accepted, the dialectical movement through sublation of contradictions "is the root of all movement and life". So Marx's dialectical matter is self-driven, multi-faceted, and at certain levels of organization capable of undergoing qualitative transitions, in which it acquires emergent properties. These properties are then subject to emergent laws that are irreducible to, and have certain autonomy from, the base laws they emerged from. Thus, Marx's materialism is non-reductive (one could say militantly anti-reductive in its revolutionary drive). Life, sentience and society are such emergent structures, and the social "superstructure", including culture, ideology, and the "ensemble of the social relations", is the autonomous, but material, realization of the historical Geist.
Some critics, e.g. Berdyaev, did charge the dialectical materialism with hylozoism (live matter-ism), suggesting that the matter like that is the spirit by another name, just a few sublations short of becoming the Nature-God of Spinoza and Goethe, and perhaps getting there along the Hegelian spiral staircase. But what distinguishes dialectical materialists from most hylozoists is their insistence on the ontological priority of the basic over the emergent, in the context of historical materialism, of the means of production over the social and cultural superstructure. What this usually means to Marx is that while the latter is autonomous and may exert some feedback influence on the former, this influence is incomparably weaker than the one going the other way, and at most may effect speed ups/slow downs or perhaps detours in the march of history, but not alter its materially determined thrust and direction.