The Brazilians moved to 13 points from five matches, with Pirates remaining top on goal difference. Both sides have also reached the MTN8 final, which will be played on October 10.
Sundowns were made to work by a competitive Milford side, who suffered their first defeat of the campaign.
After Sunday's demanding MTN8 semi-final against Golden Arrows, Miguel Cardoso rotated his team, but brought Teboho Mokoena on at half-time to help regain control after Milford created several chances.
Yanelisa Nomandela tested Ronwen Williams from distance, while Thabana Mabena came close when his effort struck the goalkeeper in the face. At the other end, Milford goalkeeper Siphamandla Hleza and his defence frustrated Sundowns, with Olwethu Cele clearing Tashreeq Matthews' effort off the line.
Sundowns finally broke through in first-half stoppage time. Aubrey Modiba won possession near the byline and supplied Iqraam Rayners, whose initial effort was saved by Hleza before the striker converted the rebound.
Milford continued to threaten after the restart, with Williams forced into another save from Bulelani Sigomoshe.
Sundowns gradually increased the pressure, although Rayners was denied after rounding Hleza and Cassius Mailula also went close.
The second goal arrived in the 76th minute when Modiba released Antonio Van Wyk, who calmly found the bottom corner for his first league goal for Sundowns.
The hosts saw out the closing stages to secure the clean sheet and three points, keeping them firmly in the title race.
Milford remain fifth on seven points and visit Chippa United on Saturday, while Sundowns travel to Golden Arrows on Sunday.
