In the wake of the loss, the Braamfontein-based side remain in second spot with 57 points and trail the new league champions by 11 points with one match to go.
With the win, Sundowns (on 68 points) remain on course to break the points tally record set by Kaizer Chiefs last season, after they managed to accumulate 69 points in the 16-team format.
The Clever Boys started like a house on fire in the opening 10 minutes and Sifiso Hlanti’s cross called Denis Onyango to action, but the goalkeeper collected the ball in the box.
After 25 minutes in the tie, Billiat spotted keeper Moeneeb Josephs off his line and produced a long range shot, beating the Clever Boys net minder and handing the Brazilians the lead against the run of play.
Four minutes later, Gavin Hunt’s men were awarded a set piece in a good position when Tebogo Langerman fouled Elias Pelembe, but Daine Klate’s attempt went over the bar.
In the 39th minute, Leonardo Castro missed twice to double the lead in a one-on-one situation with Josephs – the keeper initially saved Castro’s shot before the Colombian missed on the second invitation.
Ben Motshwari came close to finding an equaliser in the final minutes of the first half when he was set up by Sibusiso Vilakazi, but the midfielder ballooned his shot wide.
It was 1-0 at the interval to Pitso Mosimane’s side.
The hosts continued their dominance in the second half with Onyango making a brilliant save to deny Bongani Khumalo from a point blank range early on.
Towards the 70th minute, Sundowns were forced to try long range shots and Langerman’s effort couldn’t trouble Josephs as it went wide.
With Wits piling on the pressure, Onyango produced another wonderful save to deny substitute Joaquim Lupeta in the box from a sweet cross by Pelembe.
The last 10 minutes of the contest saw the Tshwane side enjoying possession and in the end the hosts failed to beat the big Ugandan goalkeeper Onyango.
The victory elevates the already crowned league champions to 68 points.