According to Shivaji and his times, by the historian Jadunath Sarkar,
On 24th March, 1680, the Rajah was seized with fever and dysentery. The illness continued for twelve days. Gradually all hopes of recovery faded away, and then, after giving solemn charges and wise counsels to his nobles and officers, and consoling the weeping assemblage with assurances of the spirit's immortality in spite of the perishableness of the body, the maker of the Maratha nation performed the last rites of his religion and then fell into a trance, which imperceptibly passed into death.
So it seems he died from dysentery, which was undoubtedly a far from uncommon occurrence in a time before antibiotics.
Sarkar goes on to say that there were rumours of poison following the death of Shivaji, but points out that there is no evidence to support those rumours. He then wryly observes that:
"Readers of Macaulay's account of the death of Charles II. will remember how at that very time in Europe hardly a sovereign died without the event being ascribed to poison."