He finished the course in a time of 1:50:21.
However, golden boy Brownlee continued England's golden start to the Commonwealth Games.
Olympic champion Brownlee, 24, duelled with younger brother Jonathan for much of the race but pulled away when he upped the pace over the last five kilometres to take the gold.
He crossed the finish line in 1:48:50 at the Strathclyde Country Park, 11 seconds ahead of his sibling.
Murray finished strongly to take the bronze.
Earlier, England's Jodie Stimpson claimed the first gold medal at the Games with victory in the women's triathlon.
With Stimpson's compatriot Vicky Holland finishing third, England took four medals from the Games' first two medal events.
Commonwealth Games podiums in Glasgow on Thursday:
Gold: Jodie Stimpson (ENG)
Silver: Kirsten Sweetland (CAN)
Bronze: Vicky Holland (ENG)
Gold: Alistair Brownlee (ENG)
Silver: Jonathan Brownlee (ENG)
Bronze: Richard Murray (RSA)
Men's 4000m Team Pursuit
Bronze: New Zealand
Women's 500m time trial
Gold: Anna Meares (AUS)
Silver: Stephanie Morton (AUS)
Bronze: Jess Varnish (ENG)
Men's team sprint
Gold: New Zealand
Women's para-sport sprint tandem
Gold: Sophie Thornhill and Helen Scott (ENG)
Silver: Aileen McGlynn and Louise Haston (SCO)
Bronze: Brandie O'Connor and Breanna Hargrave (AUS)
Gold: Kimberley Renicks (SCO)
Silver: Sushila Likmabam (IND)
Bronze: Amy Meyer (AUS) and Chloe Rayner (AUS)
Gold: Ashley McKenzie (ENG)
Silver: Navjot Chana (IND)
Bronze: John Buchanan (SCO) and Razak Abugiri (GHA)