Vincent Pule's 28th-minute strike was enough for the Clever Boys to leapfrog Pirates at the end after the Buccaneers drew 2-2 at Ajax Cape Town in their final game.
Pule got the crowd off their seats, skinning his man and firing a rocket home from 25 yards to put Wits into the ascendancy.
The home side dominated the majority of proceedings and could have been two nil up in the second half but Jabulani Shongwe missed from three yards out following Tebogo Moerane's pinpoint cross.
The game became a bit scrappy towards the end as Stars looked for a way back, with Mogakolodi Ngele forcing a save out of Moeneeb Josephs, but Wits held on to secure a third-place finish in the final Absa Premiership standings.
Wits will now have the option of entering the 2016 CAF Confederation Cup.