The British and Company forces were disordered. Many British officers had been killed or wounded, and their units were now in confusion. The British foothold included many of the liquor stores and over the next two days, many British soldiers became drunk and incapacitated on looted spirits. However, the rebel sepoy regiments had become discouraged by their defeats and lack of food, while the irregular mujahhadin defended their fortified compounds with great determination but could not be organised to make a coordinated counter-attack. Wilson eventually ordered all liquor to be destroyed, and discipline was restored. Slowly, the attackers began to clear the rebels from the city. They captured the magazine on 16 September. Another Victoria Cross was earned here, by Lieutenant Thackerey for extinguishing a fire in the magazine, whilst under musket fire. Bahadur Shah and his entourage abandoned the palace on 18 September, and a British force captured the great mosque, the Jama Masjid, and the abandoned palace the next day. They also captured the Selimgarh Fort, attached to the palace and dominating the bridge of boats over the River Yamuna. Most rebels who had not already left the city now did so before the Company forces captured all the gates and trapped them. The city was finally declared to be captured on 21 September. John Nicholson died the next day.

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