The idea is advanced that self-organization in complex systems can be treated as decision making (as it is performed by humans) and, vice versa, decision making is nothing but a kind of self-organization in the decision maker nervous systems. A mathematical formulation is suggested based on the definition of probabilities of system states, whose particular cases characterize the probabilities of structures, patterns, scenarios, or prospects. In this general framework, it is shown that the mathematical structures of self-organization and of decision making are identical. This makes it clear how self-organization can be seen as an endogenous decision making process and, reciprocally, decision making occurs via an endogenous self-organization. The approach is illustrated by phase transitions in large statistical systems, crossovers in small statistical systems, evolutions and revolutions in social and biological systems, structural self-organization in dynamical systems, and by the probabilistic formulation of classical and behavioral decision theories. In all these cases, self-organization is described as the process of evaluating the probabilities of macroscopic states or prospects in the search for a state with the largest probability. The general way of deriving the probability measure for classical systems is the principle of minimal information, that is, the conditional entropy maximization under given constraints. Behavioral biases of decision makers can be characterized in the same way as analogous to quantum fluctuations in natural systems.