Adilshah was displeased at his losses to Shivaji's forces, which his vassal Shahaji disavowed. Having ended his conflict with the Mughals and having a greater ability to respond, in 1657 Adilshah sent Afzal Khan, a veteran general, to arrest Shivaji. Before engaging him, the Bijapuri forces desecrated the Tulja Bhavani Temple, holy to Shivaji's family, and the Vithoba temple at Pandharpur, a major pilgrimage site for the Hindus.

Pursued by Bijapuri forces, Shivaji retreated to Pratapgad fort, where many of his colleagues pressed him to surrender. The two forces found themselves at a stalemate, with Shivaji unable to break the siege, while Afzal Khan, having a powerful cavalry but lacking siege equipment, was unable to take the fort. After two months, Afzal Khan sent an envoy to Shivaji suggesting the two leaders meet in private outside the fort to parley.

The two met in a hut at the foothills of Pratapgad fort on 10 November 1659. The arrangements had dictated that each come armed only with a sword, and attended by one follower. Shivaji, either suspecting Afzal Khan would arrest or attack him, or secretly planning to attack himself, wore armour beneath his clothes, concealed a bagh nakh (metal "tiger claw") on his left arm, and had a dagger in his right hand.

Accounts vary on whether Shivaji or Afzal Khan struck the first blow: Maratha chronicles accuse Afzal Khan of treachery, while Persian-language records attribute the treachery to Shivaji. In the fight, Afzal Khan's dagger was stopped by Shivaji's armour, and Shivaji's weapons inflicted mortal wounds on the general; Shivaji then fired a cannon to signal his hidden troops to attack the Bijapuri army. In the ensuing Battle of Pratapgarh fought on 10 November 1659, Shivaji's forces decisively defeated the Bijapur Sultanate's forces. More than 3,000 soldiers of the Bijapur army were killed and one sardar of high rank, two sons of Afzal Khan and two Maratha chiefs were taken prisoner.

After the victory, a grand review was held by Shivaji below Pratapgarh. The captured enemy, both officers and men, were set free and sent back to their homes with money, food and other gifts. Marathas were rewarded accordingly.