Mulaudzi latched on to double world indoor champion Abubaker Kaki of Sudan before the bell, and chased him all the way down the home straight, but Kaki held on to win in1:43.10.
Kenyan Boaz Lalang caught Mulaudzi at the line and was given second place ahead of the South African, although both were timed at 1:43.29, with Mulaudzi improving his season's best by 0.29 seconds.
Viljoen wasn't at her best, but nonetheless heaved a 59.93m effort in the fourth round to finish behind world record holder Barbora Spotakova (65.76m) and Kara Patterson of the US (64.21m).
The South African, who will defend her Commonwealth title in Delhi in October, is third in the season race with seven points.
Spotakova, the Olympic champion, leads with 12 points and Patterson is second with eight points.
Another Commonwealth Games gold medallist, LJ van Zyl, was disappointing in the men's 400m hurdles after winning the race last year in a personal best 47.94 seconds.
The 25 year old was never really in contention, finishing sixth in 49.58, almost two seconds adrift of American Bershawn Jackson who edged countryman Angelo Taylor by one hundredth of a second to win in 47.78.
Rene Kalmer put in a solid performance in the women's 3 000m race, falling eight seconds short of her career best to finish 13th in 8:52.28.
And while she trailed well behind race winner Sentayehu Ejigu of Ethiopia, who clocked a world leading 8:28.41, Kalmer will be pleased with her form as she looks for a strong showing at the African Athletics Championships in Nairobi next week where she will run the 1 500m.
Despite not reaching top form yet this season, Van Zyl will line up as favourite in the Kenyan capital, as will Viljoen as both look to defend the titles they won in Addis Ababa in 2008.
Mulaudzi will aim to improve on the silver medal he won in Algiers 10 years ago.