Security guards evacuated fans from two bays in the Bill O'Reilly Stand around 6:30pm on Friday night when the vinyl soffit sheeting began to flap precariously directly above.
The sheeting fell from the underside of the stand but did not hit anyone, with applause ringing out from those that had remained nearby.
Afterwards, the seating bays in the vicinity remained empty as security kept watch on the area, which was cordoned off with tape.
"Two seating bays have been cleared and patrons have been provided seating in another grandstand," a statement from Venues NSW said.
"As per standard processes, pre-event inspections had taken place across the venue before gates opened. Further inspections are underway. The safety of our patrons remains our number one priority."
Wild weather forced two rain delays within 45 minutes before play finally began at 7:15pm.
The conditions were so difficult Cricket Australia was unable to set up ball-tracking or ultra edge as the technology could not be calibrated in the levels of wind.
Two ground staff members were knocked off their feet in the strong winds as they attempted to pull the covers off after the first rain delay.
SCG ground staff have been working hard to clear water from the pitch ahead of Friday's BBL match. (Mark Evans/AAP PHOTOS)
The roofing incident came only one night after a small fire broke out at the Gabba during Thursday night's game between the Brisbane Heat and Hobart Hurricanes, which briefly came to a halt.
Despite the conditions, a healthy crowd was in attendance for the Sixers-Thunder match, which sold out earlier in the week.
Friday night's winner will confirm their spot in the top-two of the BBL ladder and face the Hobart Hurricanes in a grand final qualifier on Tuesday night.
The loser will finish the regular season in third place and host a knockout final on Wednesday night.
Friday's match is the last of the BBL summer for rival openers Sam Konstas and Steve Smith, who fly out for the Test tour of Sri Lanka this weekend.
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