This study presents an innovative procedure to derive the ultimate load capacity of a pile system by considering the natural (intrinsic) variability of a tropical soil. The tropical soil has high aluminum and iron content due to processes of lixiviation of the upper soil layers. As a consequence, this soil has a porous cemented structure, high void ratio, high permeability, and high variability of the geotechnical parameters in its depth. Soil layers are experimentally characterized via standard characterization, a triaxial test, standard penetration test, and flat dilatometer tests. Also, the load test of the standard groups (PG) and pile plus pile-cap (PC), which had self-drilling piles, were performed at real scale. Afterwards, simulations using a three-dimensional finite-element method (3D FEM) considering variations in soil parameters were performed for a hypothetical piles-plus-pile cap system under vertical loading using the random finite-element method. Mean parameters were verified through laboratory and field tests. Results from the load test simulations were compared with real-scale tests conducted in this study. The relative importance of variability of several geomechanical parameters was analyzed in terms of their effects on the contribution of the pile cap to the ultimate bearing capacity of the full system and found to be 18%; the minimum contribution is 2% of the total load. Finally, it is shown that reasonable savings in construction costs accompanied by a modest reduction in the safety factor (FS=1.8) may occur when the variability of parameters is taken into account.