A serious-looking injury to Ekitike compounded a miserable night for the English champions as Ousmane Dembele's double sealed a 2-0 win at Anfield for the holders, who progressed to the semi-finals 4-0 on aggregate.
The former PSG striker crumpled in a heap, holding his lower right leg with a suspected ruptured Achilles tendon that could also end his hopes of representing France at the World Cup.
"It looks really bad, but difficult for me to say how bad," said Slot.
"Tomorrow, we will investigate this further. Let's see, but it doesn't look good."
Slot had paired Ekitike up front alongside Alexander Isak, who was making his first start since breaking his leg in December.
Injuries have been a major factor in a disastrous season for the Reds as they sit fifth in the Premier League and will end the campaign without silverware.
"Losing a player is something we have had many times this season, but it is especially hard for him because you never want to be injured, especially at this time of the season," added Slot.
"The good thing is Alex is back."