The two girls were just eight and 10 years old when the alleged offending began.
Judge Bruce Davidson retired the jury after the outburst, with one member comforting another juror as they exited the courtroom.
The outburst had a palpable impact on the court, Judge Davidson said, and after deliberation in chambers the jury was dismissed entirely.
The accused, who has name suppression, now faces a judge-alone trial on multiple charges of rape and unlawful sexual connection.
The court will hear from 11 Crown witnesses over what is estimated to be a six-day trial, the first witness being a teenage girl.
The video was of the oldest of the alleged victims, who was just 15 at the time of the recording.
She outlined the alleged abuse she and the other victim faced at the hands of the man they trusted.
"We were sexually abused for years," she said. "He didn't just rape me physically, he raped me mentally."
These statements, and many details of the alleged sexual abuse, spurred the juror to smash his hands on the desk in front of him.
Judge Davidson acknowledged that the outburst would have an impact on the men and women remaining on the jury.
The court heard the juror could not bring an impartial view to the charges because he had a granddaughter of a similar age.
"His anger was palpable," Judge Davidson said.
"His reaction was human and clearly has a granddaughter of a similar age... but I have decided the best course of action is to discharge you as a whole from dealing with the case, from the impact that this would have had on yourselves and the ability to deal with the case properly and fairly."
Judge Davidson told the jury not to think of their attendance as a waste of time.
The trial will continue today in closed court.