Aru and Aketi in the 168-year old zoo located in the Tiergarten area of the city were spotted foaming at the mouth five days ago and stopped eating and drinking, the Daily Mail reported.
They also developed colic - a condition where they repeatedly cried out in distress.
Zookeepers believe the pair must have been poisoned by a visitor to the zoo.
The zoo said that the meat fed to the pair as part of their diet was not contaminated; the meat is eaten by all 16 big cats at the zoo and no others fell ill.
"We think that someone threw something into their enclosure," Curator Heiner Kloes was quoted by the paper as saying.
Blood samples from Aru, a male, and his sister Aketi will be required to try and identify the cause of their sudden illness.
Although the pair began making a slow recovery on Saturday they needed to regain more strength before blood samples can be taken from them, experts said.
The lions, who were born in the zoo in October 2007, need to be fit and healthy to withstand a general anaesthetic delivered via a dartgun.
It is the first incident of poisoning at the zoo in 25 years.
The Berlin Zoo is the most visited zoo in Europe with approximately 3 million annual visitors from all over the world.