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The target reliability index is a safety and economic measure used to stipulate the optimal reliability level for structural elements. The conventional load and resistance factor design (LRFD) philosophy is premised on limit state functions that ignore structural performance by disregarding the structural stored energy capacity. Indeed, two significant concerns have yet to be adequately addressed within structural failure and safety analysis. The first pertains to the careful consideration of failure modes. The second involves the relationship between target reliability and hazard intensity. The main goal of this research is to propose a new energy-based limit state function to incorporate the performance-based design and LRFD philosophies concerning the target reliability of bridge substructure systems, including piles. The proposed energy-based limit state function can thoroughly examine a structure’s behavior in the presence of a natural disaster. This study’s reliability analysis corresponds to the seismic performance levels. The elastic and plastic energy resistance of pile elements is quantified concerning the various performance levels subjected to the loading scenarios. The uncertainties of soil and structural resistance and the structure’s dynamic response are considered and a new energy-based limit state function established. To validate the proposed limit state function, several finite element method models are examined to capture the probability energy distribution for structural resistance and loading conditions. Finally, the structural target reliability indices for the bridge piles are delineated using the proposed optimization approaches.