His father being Jewish, Klemperer fled the Nazi regime with his family in 1935; they all made their way to Los Angeles, where his father obtained a conducting post. Klemperer began acting in high school and enrolled in acting courses in Pasadena before joining the United States Army to fight in World War II.
While stationed in Hawaii, he joined the Army's Special Services unit, spending the next few years touring the Pacific entertaining the troops. At the end of the war, he worked on Broadway, and the advent of rapid growth in the television industry opened new doors to him.
He is best remembered as Colonel Wilhelm Klink, the bumbling and self-serving Commandant of Stalag 13 on Hogan's Heroes, which ran on CBS from 1965 to 1971. Klemperer was very conscious of the fact that he was playing a German officer under the command of Nazis, and agreed to play Klink only on the condition that he would be portrayed as a fool who never succeeded. When Klemperer's father, the famous conductor, saw his first episode of Hogan's Heroes, he said to his son, "Your work is good...but who is the author of this material?". For his performance, Klemperer received six Emmy Award nominations for best supporting actor, winning in 1968, and again in 1969. It was on the set of Hogan's Heroes that he met actress Louise Troy, who was making a guest appearance. They fell in love, got married and eventually divorced (she died in 1994).
Klemperer reprised the role of Klink in an episode of The Simpsons in 1993 as Homer's guardian angel/spirit guide in the episode: "The Last Temptation of Homer" (episode # 5.9). According to the particular episode's DVD commentary, when he guested he had to be given a quick reminder of how to play Colonel Klink. Essentially, he imitated an imitation of the character. Additionally, he appeared in character and costume as Klink in a "Batclimb cameo" on the campy original Batman television series and as Officer Bolix in the Lost in Space episode "All That Glitters" in 1966.
An anecodote of this period that Bob Crane was fond of recalling involved Klemperer's car. Between 1970 and 1978, Klemperer owned a Mercedes Benz 6.9 V8, which was initially intended for Roman Polanski. When parked on the set of Hogan's Heroes, Crane always joked about it being "The Colonel's staff car". After Crane's murder, Werner sold his Mercedes-Benz because it brought back too many memories of his dead friend.
Werner Klemperer died from cancer on December 6, 2000, at the age of 80. His body was cremated and his ashes were scattered at sea. From 1997 until his death, Klemperer was married to African-American actress Kim Hamilton.