Background <p>Individuals with asymptomatic SARS-CoV-2 infection can unknowingly transmit the virus, yet identifying such subclinical infections in post-vaccinated populations remains challenging.</p> Methods <p>We conducted a longitudinal study of 129 infection-naïve vaccine recipients immunized with various combinations of SARS-CoV-2 spike (S) protein vaccine platforms. Sera were collected before the first dose (<i>v</i>1), at 2&#xa0;weeks (<i>v</i>7) and 6&#xa0;months (<i>v</i>8) after the third dose. Taiwan’s first major COVID-19 outbreak occurred between <i>v</i>7 and <i>v</i>8. We measured anti-nucleocapsid (anti-N) and anti-S IgG antibody titers by ELISA and assessed virus-neutralizing activity using live virus and pseudovirus assays.</p> Results <p>By developing an iterative serial screening method, we identified asymptomatic breakthrough (post-vaccination) infections among unconfirmed cases. Our <i>v</i>7-<i>v</i>8 paired cohort resolved into three distinct groups: confirmed cases (21%), asymptomatic breakthrough infections (17%), and uninfected subjects (62%). In normalized <i>v</i>8 sera, confirmed cases exhibited an anti-S⁺⁺⁺ (high) /anti-N⁺⁺⁺ (high) phenotype, while uninfected subjects showed an anti-S⁺ (low)/anti-N⁺(baseline) phenotype. Statistical analysis validated a distinct asymptomatic group characterized by an antibody profile anti-S⁺⁺ (intermediate) /anti-N⁺ (baseline).</p> Conclusions <p>This approach may enable more accurate estimates of vaccine efficacy and infection prevalence. In a spike-vaccinated population, anti-N antibody is more a potential specific marker for COVID-19 symptomatic disease than an ideal marker for SARS-CoV-2 infection. To our knowledge, this is the first preliminary report of identification of asymptomatic breakthrough infection from a well-vaccinated population using self-matched longitudinal pairs of serum samples.</p>