Holger Brandt, a famous virtuoso violinist, meets Anita Hoffman, his daughter's piano instructor, during a trip home. Impressed by Anita's talent, he invites her to accompany him on his next tour. They begin touring together and a passionate relationship ensues. Holger's wife Margit asks him for a divorce. Knowing how much Holger misses his daughter Ann Marie and son Eric, and torn with guilt for breaking up his family, Anita decides to pursue her own career and leaves Holger. Holger returns home to see his children again. He first travels to Ann Marie's school, but as she runs across the street to greet him she is hit by a car in front of his eyes. He takes the injured Ann Marie back home, and confronts his angry son in an attempt to explain his infidelity. To Holger's relief, the doctor informs him that Ann Marie will survive and eventually recover from her injuries. Margit then forgives Holger and welcomes him back into his family.
The musical duets, with Howard and Bergman, were dubbed for the soundtrack by professional musicians; however, the actors' hands show the actual music being played: Ingrid Bergman plays the full piano parts, so her hand positions are correct for the music soundtrack. Leslie Howard, however, could not play the violin, so a professional violinist — who also bore a striking resemblance to Leslie Howard — was brought in to teach him proper violin posture and bowing technique. During filming, this same musician, Al Sack, rested on his knees, out of view of the camera, and did the fingering on all of the close-ups. In the film, viewers see Sack's left hand and Mr. Howard's bowing arm and profile. Sack also doubled for Howard during the long shots in front of the orchestra.
In the crucial scene where the film's two main protagonists stand looking into the river and realize that they have fallen in love with each other, Holger Brandt makes a casual remark on "the time when Vienna was a happy city". This is taken by many to be a reference to the 1938 de facto annexation of Austria by Nazi Germany. However, Brandt's comment also features in the original, 1936, Swedish film, which predated the Anschluss. Others more accurately understand it to mean the period of one-party rule forced on Austria by the Patriotic Front, Austria's own fascist party, which took power in 1933. The remark may also refer to Vienna's previous imperial glory prior to the First World War, which led to the collapse of the Austro-Hungarian Empire.
Ingrid Bergman performed in a radio adaptation of Intermezzo on Lux Radio Theater on January 29, 1940, which also starred Herbert Marshall. She was also in another adaptation on the same show on June 4, 1945 with Joseph Cotten. On October 5, 1946, Marshall starred in an adaptation of Intermezzo on Hollywood Star Time.