Tomato (Solanum lycopersicum L.) is a globally important crop where accurate seed quality assessment is essential for uniform crop establishment. Seed vigor, a stronger predictor of field emergence than standard germination percentage, is often inadequately measured by conventional paper towel (PT) assays due to low precision and reproducibility. This study optimized a water–agar (WA) germination assay for tomato (cv. Seminis Abhilash) to provide a reliable platform for vigor evaluation. WA concentrations ranging from 0–2.0% (w/v) were compared with a PT control. While all WA media supported >80% germination by 14 days, the 0.5% WA treatment was optimal, achieving >80% germination within 7 days, with the highest final germination (95%), fastest mean germination time, and maximum vigor index. The optimized WA system was then used to evaluate dose-dependent effects of indole-3-butyric acid (IBA) and gibberellic acid (GA₃), alongside PT. Compared with PT, the WA assay provided greater precision, reflected in lower coefficients of variation, and more clearly resolved hormone dose–response trends. Optimal concentrations were identified at ~50 mg/L IBA and ~100 mg/L GA₃, which maximized seedling vigor. In contrast, the PT method produced variable results that obscured these patterns. Overall, the 0.5% WA assay enhances both accuracy and reproducibility of seed vigor testing and offers strong potential for high-throughput screening of seed treatments and bioactive compounds.