This paper introduces Deleuze's philosophy of becoming in a system theoretic framework and proposes an alternative ontological foundation to the study of systems and complex systems in particular. A brief critique of systems theory and the difficulties apparent in it is proposed as an introduction to the discussion. Following is an overview aimed at providing access to the 'big picture' of Deleuze's revolutionary philosophical system with emphasis on a system theoretic approach and terminology. The major concepts of Deleuze's ontology - difference, virtuality, multiplicity, assemblages, quasi-causation, becoming (individuation), intensity and progressive determination are introduced and discussed. Deleuze's work is a radical departure from the dogma of western philosophy that guides the foundations of science and systems theory. It replaces identity with difference and being with becoming; in other words, it provides systems theory with an ontological ground based on change, heterogeneity and the inexhaustible novelty-producing process that underlies all phenomena. The conceptual tools made available by this philosophy seem to capture the fundamental aspects of complexity and complex systems much better than the current conceptual system that is based on static transcendent ontological entities.