Chasing 141, Joburg Super Kings were 82/3 in 11.3 overs when the second rain interruption took place. However the hosts were ahead of hte DLS par score when rain arrived again which meant they won the match by 6 runs.
It was the first win of the second for Joburg Super Kings while MI Cape Town have a win and a loss in two matches.
Earlier, George Linde and Delano Potgieter stitched a terrific 39-ball 65 seventh wicket stand to lift MI Cape Town to a 140 for six.
While Linde remained unbeaten on 48, Potgieter fired a stunning 22-ball 44 lower down the order.
For Super Kings, David Wiese, Lutho Sipamla, Evan Jones and Tabraiz Shamsi picked up a wicket apiece.