A new approach of vacancy‐driven gelation to obtain chemically crosslinked hydrogels from defect‐rich 2D molybdenum disulfide (MoS₂) nanoassemblies and polymeric binder is reported. This approach utilizes the planar and edge atomic defects available on the surface of the 2D MoS₂ nanoassemblies to form mechanically resilient and elastomeric nanocomposite hydrogels. The atomic defects present on the lattice plane of 2D MoS₂ nanoassemblies are due to atomic vacancies and can act as an active center for vacancy‐driven gelation with a thiol‐activated terminal such as four‐arm poly(ethylene glycol)–thiol (PEG‐SH) via chemisorption. By modulating the number of vacancies on the 2D MoS₂ nanoassemblies, the physical and chemical properties of the hydrogel network can be controlled. This vacancy‐driven gelation process does not require external stimuli such as UV exposure, chemical initiator, or thermal agitation for crosslinking and thus provides a nontoxic and facile approach to encapsulate cells and proteins. 2D MoS₂ nanoassemblies are cytocompatible, and encapsulated cells in the nanocomposite hydrogels show high viability. Overall, the nanoengineered hydrogel obtained from vacancy‐driven gelation is mechanically resilient and can be used for a range of biomedical applications including tissue engineering, regenerative medicine, and cell and therapeutic delivery.