Spray the infected flowers and leaves with a general plant sulfur fungicide. Begin spraying as soon as the fungus appears and repeat twice weekly until the fungus is gone. Mix the fungicide with water as directed on the packaging then pour the solution into a spray bottle and apply it to the flowers. If you have more than one begonia, mix the solution in a garden sprayer and apply it with that.
Remove all fallen leaves and flowers that have collected around the base of the plant. Discard them in the trash. Cut off any infected stems or leaves and discard them as well.
Cut off all faded blooms, even if they do not show infection. The faded blooms can house the fungus and spread it. Space potted begonias at least 20 feet away from each other to prevent the fungus from spreading.