This is a very complex question, because despite Foucault's own project at times, it can be very hard to track influence as a force or an effect. However, I'd hazard to say that two features of his philosophical writing were especially important for the discipline of history.

The first is methodological (sort of). In the Archaeology of Knowledge, Foucault argues that his primary aim, at least up until this point, had been to uncover the conditions that allowed for new regimes of knowledge to flourish. Rather than following a teleological model, in which the incipient kernel of an idea could be found in a temporally-prior idea, Foucault sought to move laterally throughout a culture, and on the surfaces of that culture, to determine why systems of thought developed as they did. To offer one crude example, consider his early works on madness. Rather than offering a history of psychology as the improvement, refinement, and development of a medical practice to its present state, Foucault sought to understand the underlying premise of medical psychology itself: madness. What was madness? How was it defined? How were the "mad" treated? What is the distinction between madness and unreason? How did the idea of madness come about at all? Why and how did attitudes toward madness change? Etc.

As part of this "archaeology," Foucault refused to treat archival knowledge as a dataset to be statistically analyzed or a monument to be venerated and given causal authority. He would not ascribe to a "great persons" mindset, but he also thought history was not reporting, but analysis and interpretation. He saw human culture, whether historical or present, as a series of forces working in capillary action--indeed, this is the key contribution of his admixture of power and knowledge. If power is a series of forces that are dispersed throughout a culture, rather than a top-down dictate led by a small group, then what constitutes the "site" of historical inquiry shifts a great deal. As a consequence, the field of material available to him greatly expanded. He looked at all kinds of different material--fiction, non-fiction, policy, judicial decisions, architecture, etc. etc.--as material that both caused and was an effect of a given historical epoch. His early works were, more or less, focused on epistemological questions, but that epistemology was culturally embedded rather than abstract.

The second is more political. Like Nietzsche before him, Foucault's writing often foregrounded the nexus of power and knowledge, especially so in cases where he wrote about "oppressed" groups. The History of Sexuality, for example, opened up an entire field of inquiry by treating sexuality as a component of human life rather than a medical or moral question. There was a methodological effect to this: namely, Foucault's work provided a theoretical basis for including previously excluded voices from the historical conversation.