In 1996, Takamoto was honored by ASIFA-Hollywood with the Windsor McKay's Lifetime Achievement Award for his contributions to the field of animation. In 2001, the Japanese American National Museum heralded Takamoto for his achievements in entertainment. In 2005, he received the Golden Award from the Animation Guild, to honor his more than 50 years of service in the animation field.

A resident of Beverly Hills, Takamoto is survived by his wife, Barbara; his son Michael and step-daughter Leslie; and his brother Robert and sister Judy.