The Colombia striker damaged his left hamstring in Sunday's 2-0 league win at home to Levante, although a scan later showed the injury was not as bad as first feared when it had been thought he would be sidelined for around three weeks.
"Radamel is an important piece in our system, but we have Adrian Lopez, Diego Costa and Raul Garcia, who can all play in a similar role and all are in good shape," Atletico coach Diego Simeone told a news conference on Wednesday.
"I hope on Thursday we can show we can continue to do well despite the loss of Falcao."
Second-placed La Liga side Atletico hold a 2-0 lead from last week's first leg at the Calderon.
On the other side of the draw, holders Barcelona travel to Malaga on Thursday with Spain striker David Villa back in the side after injury.
Villa, Barca's top scorer in the Cup with five goals, was passed fit to return to action on Tuesday after recovering from a muscle strain.
The La Liga leaders play at the Rosaleda having drawn 2-2 at the Nou Camp in last week's first leg.
Malaga have included their new loan signing from Chelsea Lucas Piazon in their squad, with playmaker Isco out injured.