Sesame paste is an attractive condiment, but it is high in fat and prone to oil-sauce separation during storage. Sesame seeds were infrared roasted, pressed to remove partial oil, and then ground to produce sesame paste with 35%–55% oil content. The physicochemical properties of the partially de-oiled sesame paste, including texture, particle size distribution, rheological properties, colloidal and oxidative stability, appearance, and microstructure, were analyzed. Additionally, its antioxidant profile, comprising phenolic composition, total phenolic content, lignans content, 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging ability, and ferric-reducing antioxidant power (FRAP), was examined. Moreover, the molecular traits of sesame paste protein isolates (SPPI) in the partially de-oiled sesame paste, such as secondary structure, surface hydrophobicity, and free sulfhydryl contents, were also analyzed. Results showed that compared to the non-infrared radiation (IR) roasted paste, the IR roasted sesame paste had a more homogeneous structure, smaller particle size, and better oxidation stability. The contents of total phenolics, sesamol, β-sheet, and free sulfhydryl groups in the IR roasted paste increased by 42.44%–81.86%, 1.12–1.48 mg/g, 18.84%–51.45%, and 20.29%–40.93%, respectively; however, the α-helix content of SPPI decreased by 42.34%–55.47%. The increase of the unfolded protein and phenolic compounds in the sesame paste may determine the rheological properties and antioxidant profiles of the IR roasted sesame paste and hence its storage stability by preventing the oil from separating and oxidizing during long-term storage. The IR roasted sesame paste with 40% oil content, labeled as SPIR40, is acceptable for its good spreadability, appropriate fluidity, and high storage stability.