Ninjutsu also known as Ninja Techniques, are techniques which require chakra in order to be able to use it. These techniques allow the user to do things which they normally wouldn't be able to do. The difference between Ninjutwsu and Genjutsu is, Genjutsu places the opponent under illusions which has no physical damage to the opponent, where as Ninjutsu does. In order to use Ninjutsu you are required to use chakra, at most of the time perform hand seals to execute. Ninjutsu is extremely diverse, from the easy and simple ones that can be done almost at will, to ones as complex such as healing and elemental natures.
There are two methods to creating Ninjutsu, often known as Shape Manipulation, which deals with the physical structure and shape, form, potency, and movement of a technique. The second is known as Nature Manipulation, which is related to elemental natures. It molds the physical attributes of the chakra to turn it into an element used for a technique.
As far as elemental transformations go, there are two types, the basic five, wind, fire, water, lightning, and wind, and advanced elemental transformation requiring a combination of the basics. Similar to colors, where you mix primary colors to form secondary colors.
Apparently, the Sage of Six Paths created Ninjutsu and the concept behind it. In time, people managed to understand the teachings behind it and utilized Ninjutsu to fight. Ninjutsu can be used in collaboration with Taijutsu as well, as shown with the 4th Raikage, to create nintaijutsu, a combination of both Tai and Nin.
Chakra is the molding of physical, and natural energy. It is essential to every technique.