Andrelton Simmons, who is hitting .292 at Double-A Mississippi, was called up and is expected to take over the starting job.
General manager Frank Wren said Simmons has "special talents" at shortstop. Simmons almost beat out Pastornicky in spring training.
The team is off Thursday. Simmons will join the team for Friday's first game of a weekend series at Washington.
Pastornicky was hitting .248 with seven errors as the primary starter.
Veteran Jack Wilson started at shortstop against the Cardinals on Wednesday and had an error.