The victory moves Chiefs to 51 points from 28 games, seven ahead of fourth-placed AmaZulu with two rounds left to play. They cannot be caught in third.
Chiefs must still go to Usuthu next Saturday for what had looked like it might be the decisive fixture in that race, before the visit of relegation-threatened Chippa United on the final day.
Morris scored his first goal for Chiefs since a 2-2 draw with AmaZulu in February 2025, having been barely used in this campaign.
It was, in fact, his first league appearance of the season, to go with only one other showing in the Carling Knockout.
He turned the ball in at the back post after Glody Lilepo’s fine low cross from the right wing on 86 minutes.
Vilakazi added the second from the penalty spot to make sure of the win and continental football for the side next season.
It was not a vintage display, but the Soweto side did the job and came away with a deserved victory.
They were without the suspended Siphesihle Ndlovu, and the injured Wandile Duba and Mdu Shabalala, who have performed well for them in recent weeks.
Gaston Sirino came into the side but had an evening to forget on the whole.
He fired just wide from the left-hand side of the box, before also stinging the palms of Sekhukhune goalkeeper Toaster Nsabata with a 35-yard shot.
Sirino then fired straight at the goalkeeper with a tame effort when the ball fell to him in the box.
Glody Lilepo forced a good save from Nsabata with a typically rasping shot from 20 yards that almost snuck in at the near post, before the two late goals sealed the win.