Tebogo, 21, was able to ease up at the end and still clocked an African record of 19.46sec for gold with American Kenny Bednarek taking silver in 19.62sec and Lyles fading to bronze in 19.70sec.
The sole African to have won a short sprint title at an Olympic Games is South African Reggie Walker, over 100m at the 1908 Games in London.
The final lacked the pre-race hype of the 100m, falling mid-session at a packed Stade de France.
Lyles was given a huge reception when introduced as cameras showed him up on the big screens at either end of the stadium.
The newly crowned 100m champion was drawn in lane five, outside Alexander Ogando and inside American teammate Erriyon Knighton, while Tebogo was in seven.
The American bounded into the stadium, as he had done before the 100m final, cupping his ear to the crowd.
Tebogo, however, walked quietly on and went straight to his blocks.
After the gun went for the start, Lyles was quickly up on Ogando.
He, Tebogo and Bednarek all rounded the bend well, but coming into the home straight, Lyles was in third spot.
Tebogo looked in total control, even relaxing as he went through the finish line, making a brushing-off gesture with his hand on his sky blue vest.
Bednarek held on for silver, with Lyles prone on the track after being unable to replicate his gold medal showing in the 100m.
