The objective of this study was to evaluate whether silicon (Si) amendments, known to have a prophylactic role against biotrophic and hemibiotrophic pathogens, could protect soybean against Phytophthora sojae. To fulfill this objective, the initial challenge was to develop a method of inoculation that reproduced the natural infection process while allowing regular Si feeding to the plants. In a first set of experiments, inoculation of P. sojae zoospores directly into hydroponic solutions led to reproducible infections and expected phenotypes when using ‘Williams’ (rps), ‘L75-6141’ (Rps1a), ‘haro15’ (Rps1k), and ‘L77-1863’ (Rps1b) soybean challenged to races 3 and 7 of P. sojae. This approach offers the advantage of testing simultaneously many soybean cultivars against different races of P. sojae in a controlled environment, and the expression of partial and root resistance. In a second set of experiments aimed at testing the effect of Si, our results clearly showed that Si amendments had a significant effect on disease reduction and plant yield. The effect was particularly noticeable when combined with a cultivar displaying a certain level of resistance to the disease. These results demonstrate a useful method of direct inoculation of soybean plants with P. sojae zoospores through a hydroponic system and show that Si amendments can represent an alternative method of control of P. sojae against soybean.