Zaillian followed with the Penny Marshall-directed "Awakenings" (1990), a tear-jerking true story about a doctor's quest to cure his comatose patients, which netted a Best Screenplay Oscar nomination. At the behest of producer Scott Rudin, he made his directorial debut with "Searching for Bobby Fischer", crafting a touching father-son relationship film set against the high-tension world of competition chess. Despite its enthusiastic reception by critics, the film failed at the box office, as did another Zaillian-scripted father-son drama "Jack the Bear" (also 1993), which featured a nice performance by Danny De Vito. The success of Steven Spielberg's "Schindler's List" that same year, however, redeemed him, bringing critical kudos and numerous accolades including an Oscar for his chilling screenplay (adapted from Thomas Keneally's book) about the morally ambiguous German businessman who saved hundreds of Jews during the Holocaust. Attached to the project since the involvement of Martin Scorsese (to whom he was introduced by "Awakenings" star Robert De Niro), Zaillian rigorously concentrated on the main character yet also managed to movingly depict the enormity of the historical circumstances.
Zaillian went mainstream for his next two projects, sharing screenwriting credit with Donald Stewart and John Milius on Phillip Noyce's "Clear and Present Danger" (1994, adapted from the Tom Clancy techno-thriller), and providing the story (with David Koepp) for the Brian De Palma actioner "Mission: Impossible" (1996), which Koepp and veteran screenwriter Robert Towne fleshed out. He reportedly did some uncredited script doctoring on "Twister" (also 1996) as well as "Amistad" (1997) and "Saving Private Ryan" (1998). both directed by Spielberg, before returning behind the camera to helm "A Civil Action", a film diametrically opposed to the John Grisham "cowboy lawyer" dramas that had dominated the genre of late. A complex, compelling examination of personal injury law, it focused primarily on one man making the environmental and legal stories, even the personal tragedies, secondary to this individual lawyer's obsession with the case and the change it triggers in him. The film boasted a fine starring turn by John Travolta and even better supporting work by William H Macy and especially Robert Duvall, who was generally acknowledged as having walked off with the film.