Protein-based fat replacers are gaining attention due to their low-calorie content and increasing consumer demand for high-protein, plant-based foods. However, traditional methods require high thermal input (75–95 °C for 20–40 min) to induce protein aggregation, limiting their energy efficiency. Limited proteolysis offers an alternative by promoting aggregation under milder conditions, but the relationship between hydrolysis extent, molecular structure, and functional performance remains insufficiently understood. This study employed response surface methodology to optimize the hydrolysis of pea protein isolate (PPI) using Alcalase. The optimal condition—7.5% protein, 1.65% enzyme, and 6 minutes—produced hydrolysates (PPH) with enhanced surface reactivity, higher sulfhydryl–disulfide content, and uniform aggregation after mild heating (85 °C, 10 min). These PPH aggregates were incorporated at 0.3% into skim milk to create fat-free cream cheese. Incorporation of PPH increased moisture content from ~63% to ~70%. Rheological analysis showed that G′ decreased from 36 kPa (control) to 11 kPa (PPH), and apparent viscosity dropped by ~78%, indicating a softer and more spreadable texture. Creep-recovery testing confirmed greater compliance and delayed structural recovery in PPH-containing samples. Tribological analysis revealed significantly lower friction coefficients under boundary and mixed regimes, suggesting enhanced lubrication. Microscopy revealed a less continuous protein matrix in PPH samples, likely due to clustering and PPH–casein interactions. These findings suggest that limited proteolysis enables precise modulation of plant protein structure and functionality. PPH produced under optimized conditions hold promise as energy-efficient, plant-based fat replacers with favorable rheological and lubrication properties for low-fat dairy applications.