Pellegrini has preferred Costel Pantilimon to the England international in the last month, with Hart dropped after his last-minute mistake allowed Fernando Torres to score the winner in City's 2-1 defeat to Chelsea on 27 October.
Romania keeper Pantilimon has performed well in his place and kept his third clean sheet in five outings as City thrashed Tottenham 6-0 on Sunday.
But speaking after the game at the Etihad Stadium, Pellegrini made it clear Hart would return against the Czech side.
"Joe Hart will play on Wednesday," he said.
Manchester City's game with Viktoria Plzen will be shown on Sky Sports 4 HD from 7:30pm on Wednesday.