The strait is an important regional shipping route in Southeast Asia.

Ports along the strait include Balikpapan and Bontang in Borneo, and Makassar, Palu, and Parepare in Sulawesi.

The International Hydrographic Organization (IHO) defines the Makassar Strait as being one of the waters of the East Indian Archipelago.

By a line joining Tanjong Mangkalihat, Borneo (1°02′N 118°57′E / 1.033°N 118.950°E / 1.033; 118.950) and Stroomen Kaap (Cape Binar), Celebes (1°20′N 120°52′E / 1.333°N 120.867°E / 1.333; 120.867).

The arrival of the Benggai Sula microplate has rotated the Island of Sulawesi in a counter-clockwise direction, allowing opening of the southern Makassar Basin with accommodation by the Adang/Paternoster Fault.