We measure the in-plane distribution of thermally activated vortices in a trapped quasi-2D Bose gas, where we enhance the visibility of density-depleted vortex cores by radially compressing the sample before releasing the trap. The pairing of vortices is revealed by the two-vortex spatial correlation function obtained from the vortex distribution. The vortex density decreases gradually as temperature is lowered, and below a certain temperature, a vortex-free region emerges in the center of the sample. This shows the crossover from a Berezinskii-Kosterlitz-Thouless phase containing vortex-pair excitations to a vortex-free Bose-Einstein condensate in a finite-size 2D system.