Head coach Ruben Amorim has confirmed the Dutch defender, who joined him at the pre-match press conference, will be in the XI for the 17:45 GMT kick-off.
Malacia made his comeback from a lengthy injury lay-off in our previous match in this competition, the 3-2 home victory over Bodo/Glimt.
A 24-man squad flew to Prague on Wednesday afternoon, ahead of the game, with only Luke Shaw and Jonny Evans of the senior members of the first-team squad unavailable.
Evans was spotted in training at Carrington and may be hoping to prove his fitness for the upcoming fixtures, starting with the derby against Manchester City at the Etihad Stadium on Sunday.