Brendan Rodgers’ troops are due to kick-off their group-stage bid next Tuesday against the winners of the clash between Northern Irish champions Linfield and minnows La Fiorita of San Marino.
But there are now concerns over their Belgian centre-back’s availability after Boyata suffered a twisted knee just moments before half-time.
The 26-year-old’s discomfort was clear for all to see at the Czech side’s Eden Arena home and he failed to reappear after the break as he was replaced by Jonny Hayes.
The Hoops dominated Slavia but were held to a stalemate for the second warm-up match running.
Tom Rogic and James Forrest both had decent efforts at goal during the opening 45 minutes but could not beat Slavia keeper Jan Lastuvka.
Scott Sinclair was guilty of missing from point-blank range early in the second period while Callum McGregor also fluffed his finish after his solo run took him past a clutch of defenders.