Thys, making a comeback after he was cleared in February from a doping case that dragged on for six years, finished fourth in his maiden ultra-marathon as Muzhingi bagged his first Two Oceans title.
The 40-year-old South African had said ahead of the race he would challenge the course record set by Thompson Magawana in 1988.
After finishing more than six minutes off the pace, in 3:09.42, Thys said he would aim for the Comrades 'down' run mark of 5:20.49, set by Russian Leonid Shvetsov in 2007, in the annual pilgrimage between Pietermaritzburg and Durban in June.
" I know a record is possible on this course, but the weather conditions were against us today," Thys said.
"I congratulate Stephen on his win, but I will be back to race him in Comrades.
"I am going for the record. Five hours is a jogging pace, and I promise you I will be taking the fast bus to the finish."
Muzhingi slipped and fell on the muddy grass at the University of Cape Town, after more than 12 000 half-marathon runners had passed through earlier in the day, in cold, wet conditions, but he picked himself up to cross the line in 3:08.08.
The Zimbabwean became the first man since Derek Preiss in 1974 to hold the Comrades and Two Oceans titles at the same time.
"This is part of my build-up to Comrades," Muzhingi said.
"I was going for a time, and I knew that it was a time good enough for victory."
Henry Moyo of Malawi came through in the dying stages to steal second place in 2:08.35, with Muzhingi's countryman, Collen Makaza, taking third in 3:08.45.
Thys, in fourth, was the first of five South Africans among the gold medallists.
Elena Nurgalieva coasted to her fourth victory in the women's race, in the absence of injured twin sister Olesya, in 3:41.55.
Former champion and fellow Russian Natalia Volgina slowed in the last 10km, after holding on to Nurgalieva for most of the race, to finish second in her first ultra-marathon in nine years.
"It is always a help to have company and someone to talk to so I want to thank Natalya," Nurgalieva said.
Volgina crossed the line in 3:45.29 and American Devon Crosby-Helms was third in her Two Oceans debut in 3:47.30.
Adinda Kruger was the first South African home, finishing sixth in 3:50.13.
Local runners dominated the half-marathon, with Xolisa Tyali breaking clear in the approach to the finish, holding off challenges from Joel Mmone and Lucky Mohale to win in 1:04.54.
Rene Kalmer comfortably won the women's race, smiling and waving to the crowd at UCT before she crossed the line in 1:15.02.
Results of the Two Oceans ultra-marathon and half-marathon in Cape Town on Saturday (RSA unless otherwise stated).56km: Men: 1 Stephen Muzhingi (Zim) 3:08.08, 2 Henry Moyo (Mal) 3:08.35, 3 Collen Makaza (Zim) 3:08.45, 4 Gert Thys 3:09.42, 5 Bongumusa Mthembu 3:10.16, 6 Mthandazo Qhina 3:11.00, 7 Tsotang Maine (Les) 3:11.51, 8 Lucas Nonyana 3:12.03, 9 Odwa Tunyiswa 3:12.50, 10 Kimutai Lezan (Ken) 3:12.58
Women: 1 Elena Nurgalieva (Rus) 3:41.55, 2 Natalia Volgina (Rus) 3:45.29, 3 Devon Crosby-Helms (US) 3:47.30, 4 Mamorallo Tjoka (Les) 3:48.50, 5 Samukeliso Moyo (Zim) 3:49.10, 6 Adinda Kruger 3:50.13, 7 Lizih Chikore (Zim) 3:52.26, 8 Ntombesintu Mfunzi 3:52.39, 9 Tshifhiwa Mundalamo 3:53.00, 10 Paulina Njeya 3:53.29
21km: Men: 1 Xolisa Tyali 1:04.54, 2 Joel Mmone 1:05.01, 3 Lucky Mohale 1:05.09, 4 Tshamano Setone 1:05.22, 5 David Manya 1:05.50
Women: 1 Rene Kalmer 1:15.02, 2 Irvette van Blerk 1:16.22, 3 Rutendo Nyahora 1:18.30 (Zim), 4 Zintle Xiniwe 1:19.39, 5 Christine Kalmer 1:20.05