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I have two file, video.mp4 and audiotrack.mp3. I am using the following command to insert the audio with the video to create an audio track in the video, and it's working.

ffmpeg -y -i video.mp4 -i audiotrack.mp3 -af apad -map 0:v -map 1:a -c:v copy -shortest finalwithAudio.mp4

The problem: The audio works fine but ends aburptly when the video reaches its end. I want it to start fading out 1 or 2 seconds before the video end. is it possible?

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Use the afade filter. Assuming video.mp4 is 10 seconds long and a fade of 1 second is wanted:

ffmpeg -i video.mp4 -i audio.mp3 -af "apad,afade=type=out:start_time=9:duration=1" -c:v copy -shortest output.mp4

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