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Use the Stereo Rectify function to calculate the R1, R2, P1, P2 matrices of the stereo system. Along with all the other outputs of Stereo Calibrate.
Then, use the function undistortPoints in imgProc that takes the camera matrix, distortion matrix, R and P for that camera and properly undistorts them. I don't know why there's not at least a reference in the camera calibration module.
