The benchmark Hang Seng Index rose 0.28 percent, or 72 points, to 25,893 points despite the anti-mask law chaos. Mainland shares also posted gains after the Golden Week.
MTR Corporation (0066) shares slid 0.11 percent to HK$43.60 yesterday, and Best Mart 360 (2360), with stores severely damaged in the protests, declined 9.45 percent to HK$1.82.
Index heavyweight Tencent Holdings (0700) rose 0.31 percent to HK$323.80.
Pharmaceutical firms gained, with CSPC Pharmaceutical Group (1093) climbing 6.88 percent to HK$17.10, making it the biggest percentage winner among blue chips. Sino Biopharmaceutical (1177) also rose 2.75 percent to HK$10.48.
Local developers continued to bear the brunt of weak market sentiment. New World Development (0017) lost the most among blue-chips, sliding 2.5 percent to HK$10.14, while Link Real Estate Investment Trust (0823) fell 2.4 percent to HK$85.35.
Asian shares inched up, with Chinese shares making modest gains after the week-long holiday, though investors remain cautious over US-China trade talks after President Donald Trump said a quick trade deal was unlikely.
The SSE Composite Index rose 0.29 percent to 2,913 points and the SZSE Component Index edged up 0.30 percent to 9,474 points.