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Van Niekerk took the lead out over the first bend and the back straight before the Grenadian pulled away over the final 150m with the South African challenging till the bitter end for a time of 44.68 sec.
Lalonde Gordon of Trinidad and Tobago posted a time of 44.78 seconds to finish in third place.
The Commonwealth silver medal completes a magnificent year for the Bloemfontein athlete after sensationally breaking the 15-year-old national record at the Diamond League meeting in New York in June with a time of 44.38 seconds.
Van Niekerk has another possible chance of winning silverware as he will feature in the 200m semi-finals along with compatriots Ncincilili Titi and Akani Simbine on Thursday.
The country's first field event medals came courtesy of the long jump duo of Zarck Visser and Rushwahl Samaai as they claimed silver and bronze respectively.
Olympic champion Greg Rutherford of England clinched the gold medal with a winning distance of 8.20m.
Visser leapt into second place with his best effort of 8.12m, while Samaai's 8.08m attempt earned him third place.
South African javelin queen Sunette Viljoen surrendered her Commonwealth title to Australia's Kim Mickle,who also smashed Viljoen's Games record with a heave of 65.96m.
Viljoen was on the cusp of winning her third consecutive Commonwealth gold medal but her 63.19m was only good enough for a creditable silver medal.
Kelsey-Lee Robberts of Australia rounded off the podium with a best heave of 62.95m.
Meanwhile, South African men's 800m ace Andre Olivier booked a final berth in two-lap race after finishing third in his semi-final in a time of one minute, 46.30 seconds (1:47.93).
He will face world record holder David Rudisha and Olympic silver medallist Nijel Amos of Botswana.
South African discus thrower Victor Hogan also progressed to Thursday's final with an automatic qualification in the morning session.
Commonwealth Games podiums in Glasgow on Wednesday:
Athletics
Women's 3000m steeplechase
Gold: Purity Cherotich Kirui (KEN)
Silver: Milcah Chemos Cheywa (KEN)
Bronze: Joan Kipkemoi (KEN)
Men's long jump
Gold: Greg Rutherford (ENG)
Silver: Zarck Visser (RSA)
Bronze: Rushwahl Samaai (RSA)
Men's 400m
Gold: Kirani James (GRE)
Silver: Wayde van Niekerk (RSA)
Bronze: Lalonde Gordon (TRI)
Heptathlon
Gold: Brianne Theisen-Eaton (CAN)
Silver: Jessica Zelinka (CAN)
Bronze: Jessica Taylor (ENG)
Women's Javelin
Gold: Kim Mickle (AUS)
Silver: Sunette Viljoen (RSA)
Bronze: Kelsey-Lee Roberts (AUS)
Diving
Women's synchronised 10m platform
Gold: Meaghan Benfeito/Roseline Filion (CAN)
Silver: Sarah Barrow/Tonia Couch (ENG)
Bronze: Pandelela Tinong Pamg/Nur Sabri (MAS)
Men's 1m springboard
Gold: Jack Laugher (ENG)
Silver: Matthew Mitcham (AUS)
Bronze: Grant Nel (AUS)
Women's 3m synchronised springboard
Gold: Alicia Blagg/Rebecca Gallantree (ENG)
Silver: Jennifer Abel/Pamela Ware (CAN)
Bronze: Maddison Keeney/Anabelle Smith (AUS)
Gymnastics
Men's individual all-around final
Gold: Max Whitlock (ENG)
Silver: Daniel Keatings (SCO)
Bronze: Nile Wilson (ENG)
Wrestling
Women's freestyle -53kg
Gold: Odunayo Adekuoroye (NGR)
Silver: Lalita Lalita (IND)
Bronze: Jill Gallays (CAN) and Mpho Madi (RSA)
Men's freestyle -61kg
Gold: David Trembley (CAN)
Silver: Bajrang Bajrang (IND)
Bronze: Amas Daniel (NGR) and Viorel Etko(SCO)
Women's freestyle -58kg
Gold: Aminat Adeniyi (NGR)
Silver: Sakshi Malik (IND)
Bronze: Tayla Ford (NZL) and Braxton Rei Stone (CAN)
Men's freestyle -97kg
Gold: Arjun Gill (CAN)
Silver: Satywart Kadian (IND)
Bronze: Leon Rattigan (ENG) and Sam Belkin (NZL)
Women's freestyle -69kg
Gold: Dori Yeats (CAN)
Silver: Angele Tomo (CMR)
Bronze: Navjot Kaur (IND) and Hannah Rueben (NGR)
Weightlifting
Women's +75kg
Gold: Maryam Usman (NGR)
Silver: Ele Opelege (SAM)
Bronze: Tracey Lambrechs (NZL)
