Tomato (Solanum lycopersicon) is a widely produced and consumed fruit vegetable worldwide. Silicon (Si) and selenium (Se) can promote crop growth and development. However, the effects of these elements on tomato fruit quality have not been investigated comprehensively, nor are their combined effects on yield and quality clear. The aim of this study was to investigate the effects of foliar application of Si and Se on tomato growth, yield and fruit quality. The tomato plants were foliarly applied with 1 mM Si and 25 μM Se individually or in combination, and the experiment was carried out in a plastic arch shed at Yangling in spring. Our results demonstrated improved plant growth by application of Si and Se, with the effect of combined treatment being more obvious. Application of Si individually or in combination with Se increased the yield. Se addition increased the concentrations of soluble sugars, vitamin C, phenols, anthocyanin, lycopene, carotenoids, Se and protein, and decreased the nitrate level, but did not affect the concentration of total organic acids in the fruit. Si application induced similar changes to Se addition in the levels of sucrose and protein in the fruit, but had no effect on other quality traits. The combined Si and Se treatment did not show significant superior effects on the fruit quality over their individual applications. Our results suggest that Si and Se application improved the tomato plant growth. Si and Se application, respectively, had obvious effects in the yield increase and quality improvement, and the combined treatment had positive effects on both aspects. The study may provide a theoretical base for the application of Se and Si fertilizers in tomato production.