After a pause of around 20 minutes, Franklin resumed the battle by firing on the Defence and Swiftsure, but her resistance was largely spent and she struck after the loss of both main and mizzen masts.

Tonnant, Heureux, Mercure and Alexander all continued to drift towards the French rear, with Alexander anchoring shortly after midnight. Firing had largely ceased by 3:00 am, the crews falling into exhausted sleep by their guns.

The break of dawn at 5:00 am showed a scene of absolute devastation. The French van and centre had been destroyed, with only the rear squadron under Villeneuve intact. Nelson   ordered the least damaged British ships to move downwind and mop up resistance. 
"Victory is not a strong enough word for such a scene"
Nelson, on seeing the bay at dawn 
Seeing the frigate Justice set sail and fearing that the dismasted Bellerophon was under threat, Nelson ordered the Zealous to intercept. From Villeneuve's later correspondence, this appears to have convinced him that enough British vessels were still sufficiently mobile to cut off his escape from the bay and increased his hesitation as to what to do next. As noon approached, he finally took his chance.
Noon on 2nd August 1798.  At top right, Villeneuve (red) leads his remaining 4 ships from the bay. Just below Zealous is obeying Nelson's signal of recall having suffered heavy rigging damage trying to prevent the escape. The British  have now formed an inpromptu battleline in the centre, with only the French Timoleon and Tonnant still resisting. Tonnant eventually surrenders on  the morning of the 3rd August. The explosion of Timoleon, set on fire by her departing crew,  signals the bitter end of the battle.