The French fell back some 3km and attempted to regroup to hold the village of San Giuliano. Outnumbered and driven from their best defensive position, the battle was as good as lost.

Melas, who was injured when his horse was shot out from under him, and 71 years old, handed over command of the persuit to his chief of staff, Anton von Zach, and Konrad Valentin von Kaim. Valuable time was wasted in reorganising the Austrian centre into a column. Meanwhile, the entire division of the Austrian left under O'Rielly became absorbed in pursuing and capturing a detachment of 300–400 French soldiers at Cassina Bianca. This took his troops out of supporting distance from the Austrian main body. On the Austrian left, Ott hesitated to press hard against the French because Jean Rivaud's small brigade of French cavalry hovered to the north.

Meanwhile Desaix hastened his advance. Shortly before 5pm, he reported to Bonaparte in person with the news that his force (6,000 men and 9 guns of Boudet's division) was not far behind. The story goes that, asked by Bonaparte what he thought of the situation, Desaix replied: "This battle is completely lost. However, there is time to win another."