The Ilmen-Vishnevogorsky and Buldym carbonatite complexes occurring in the Southern Urals represent linear deformed carbonatite complexes. Their origin, as well as the age and geodynamic conditions remain the subject of debate. The isochron methods (Rb-Sr, Sm-Nd, TIMS) and local U-Pb-dating of zircons (SHRIMP II and LA-ICP MS) of these carbonatite complexes were employed to determine the age and duration of the stages of alkali-carbonatite magmatism and associated rare-metal ore formation. The Silurian-Devonian U-Pb zircon ages of the early phases of Ilmen-Vishnevogorsky miaskites and carbonatites were determined as 420.7±11 Ma (S2) and 417±2.8 Ma (D1), respectively. In the later phases of miaskites and carbonatites, early zircons are resorbed, they have broken isotope systems, and later zircon generations form a cluster of 386±7.6 Ma (D2). The Lower Permian U-Pb age of zircon 280±8 Ma (P1) was determined in the miaskite-pegmatite and late carbonatite. The isochron dating of late ore-bearing varieties of carbonatites provided the ages from the Lower Permian to the Early Triassic (P1–T1): 254±18 Ma, Sm-Nd and 247±4 Ma, Rb-Sr, IVC; 280±53 Ma, Sm-Nd, Buldym complex. Thus, the generation and intrusion of alkaline magmas in the Urals occurred ~420 Ma (S2–D1), synchronously with the formation of island-arc complexes. They are related to rifting on the emerging continental margins. The tectonic activity and formation of alkaline rocks and carbonatites proceeded in the Middle Devonian (~380 Ma, D2); it correlates with the accretion-collision stage of the Urals development. At the stage of "hard" collision (~280 Ma, P1), the Ilmen-Vishnevogorsky and Buldym complexes were plastically deformed, underwent melting and emplaced conformably with collision-slip tectonic structures. Recrystallization of rocks and minerals, plastic and brittle deformations, processes of pegmatitic, carbonatitic and rare-metal ore formation are associated with palingenic-metasomatic transformation of rifting alkaline complexes of Silurian-Devonian age at the collision and post-collision (~250 Ma, P3–T1) stages of the Urals emplacement.