We succeeded in measuring phase shift spectra of a microsphere cavity coupled with a tapered fiber using a weak coherent probe light at the single photon level. We utilized a tapered fiber with almost no depolarization and constructed a very stable phase shift measurement scheme based on polarization analysis using photon counting. Using a very weak probe light (bar{n} = 0:41), we succeeded in observing the transition in the phase shift spectrum between undercoupling and overcoupling (at gap distances of 500 and 100 nm, respectively).We also used quantum state tomography to obtain a purity spectrum. Even in the overcoupling regime, the average purity was 0.982 pm 0.024 (minimum purity: 0.892), suggesting that the coherence of the fiber-microsphere system was well preserved. Based on these results, we believe this system is applicable to quantum phase gates using single light emitters such as diamond nitrogen vacancy centers.