Son capitalised on a mistake by Bjorn Engels to slot pass Pepe Reina in the 94th minute and secure all three points for Spurs.
It was Son’s second goal in the game after he put Spurs 2-1 ahead on the stroke of half-time.
Also on target for Spurs was Toby Alderwereld, who drew his side level on 27 minutes after his own goal on nine minutes had put Villa 1-0 up.
Before his mistake, Engels had equalised for Villa in the 53rd minute.
The win took Spurs to 40 points on fifth position, just a point behind fourth placed Chelsea.
Villa sit 17th on 25 points and one point above the relegation zone.
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