Milford will play a first ever season in the top division and add another club from the KwaZulu-Natal province to the 16-team league, joining AmaZulu, Lamontville Golden Arrows, Durban City and Richards Bay.
Magesi will be disappointed by their failure having led in the game, but were unable to hold on for the win that would have kept them up.
Magesi took the lead through former Kaizer Chiefs forward Edmore Chirambadare, before Milford missed a penalty via Cheswyn Philander late in the first half.
That did not prove costly though as Menzi Chili netted in the second period to give them the point they needed to top the table.
Milford have owner-coach Xanti Pupuma in charge and first appeared on the south African football map when they reached the Nedbank Cup Last 32 in 2016.
The club continued to campaign in the lower leagues until they purchased the status of Uthongathi FC, elevating them to the second tier for the 2023/24 campaign.
They caused one of the great Nedbank Cup upsets in 2024 when they ousted Kaizer Chiefs on penalties in the Last 32.
They reached the semi-finals again in 2026 but lost on penalties to TS Galaxy.