The actor became obsessed with Kapoor's famously heavily-lined eyes after she first adopted the look in romantic thriller Kurbaan, according to Mumbai Mirror.
Khan and Kapoor are to next appear together in Sriram Raghavan's Agent Vinod.
On her look for the film, Kapoor told the newspaper: "I can't reveal any details on the character but I can say that Saif likes me with my eyes made up like I had done in Kurbaan.
"Sometimes I do up my eyes that way when I attend functions with him. You could say that he has designed this look for me even in Agent Vinod."