Chawrasia shot six-over 77 in the first round at the par-71 West Course. He was the only Indian in the field.
South Africa's Wallie Coetsee moved into a one shot lead as the home contingent look to continue their remarkable record at the Joburg Open.
First round leader Nic Henning shot 78 in the second round after a first round 62. He was tied 75th and missed the cut.
The 42 year old Coetsee, who ended a 17-year title drought on the co-sanctioning Sunshine Tour with a win in Zambia last year, added a six under par 65 on Royal Johannesburg & Kensington's West Course to his opening 66 on the East Course for a 12 under halfway total.
Dyson put himself in contention for a first European Tour title in four years as he added a five under par 67 on the East Course to his opening 65 on the West Course - the bumper 210-man field tackle both courses over the first two rounds before the final 36 holes take place on the more demanding East layout.
The six-time European Tour winner birdied five of his first ten holes before dropping his only shot of the day at the 12th, but converted from 15 feet for a gain at the 17th.
