$ ffmpeg -i video.mp4 -i audio.wav \
-c:v copy -c:a aac -strict experimental output.mp4
$ ffmpeg -i video.mp4 -i audio.wav -c copy output.mkv
$ ffmpeg -i video.mp4 -i audio.wav \
-c:v copy -c:a aac -strict experimental \
-map 0:v:0 -map 1:a:0 output.mp4
Source: https://superuser.com/a/277667