Both: Asian elephant (both have Southeast Asian, Antwerp also has non-subspecific); Java mouse deer; giraffe; okapi; Reeve’s muntjac; Himalayan tahr; red duiker; hippopotamus
Antwerp
? Yellow-spotted rock hyrax (if included)
Hartmann’s mountain zebra
Malayan tapir
Balabac mouse deer
Mishmi takin; Cape buffalo; eastern bongo
Berlin
Przewalski’s horse; Grant’s and Grevy’s zebras
Baird’s and Brazilian tapirs
Eastern black and greater one-horned rhinoceroses
Red river hog; Bornean bearded and Negros warty pigs; northern warthog; Sulawesi babirusa
Southern white-lipped peccary
Guanaco; vicuna
Chinese water, Persian fallow, Visayan spotted, white-tailed and Indian swamp deer; Japanese sika: southern pudu; Eurasian forest reindeer
Blackbuck; springbok; southern gerenuk; Kirk’s dik-dik; Sichuan takin; Siberian ibex; lowland anoa; Indian gaur; Javan banteng; plains and European bison; forest buffalo; nyala; western sitatunga; greater kudu; common eland; eastern bongo; defassa waterbuck; Kafue lechwe; black sable antelope; gemsbok; scimitar-horned oryx; blesbok;
Western pygmy hippopotamus
Antwerp has a hyrax, but Berlin has rhinoceroses, pigs and a peccary, as well as a far better collection of deer and bovids. Antwerp was the first continental zoo I visited and I remember it had a nice collection of cattle, but now just has 1 species.
An easy win for Berlin.