In the field of bridge structural system identification (SSI), Bernoulli beam element models are often used to solve inverse problems. More rarely, Timoshenko beam element models can be calibrated. However, these models account for only the general shear effects, whereas other shear effects, such as shear lag, are not accounted for. However, as wide-flange box girder bridges become prevalent due to design demands, neglecting shear lag may introduce significant errors in predicting the mechanical parameters of the system and, hence, reduce the accuracy. In this paper, for the first time, the shear lag's effect on the vertical deflections is taken into account in an inverse problem. A parametric SSI, the observability method (OM), is updated to address the identification of thin-walled box girder bridges with wide flanges, including the shear lag effects. The structural analytical equations are used to connect the spatial shear effects with the beam-unidimensional-element model to be applied in the inverse analysis, which is referred to as the analytical observability method (AOM-SSI). This updated version of the OM is established and validated to identify the mechanical parameters of a structural test. The identified mechanical parameters show much better agreement with the expected results than those obtained with previous methods.