The all-rounder would get all the support he needed from the team, he said.
"It's disappointing and a big loss to the team to be without him in the starting line-up," said Pybus.
"We've got three important games left and will have to reset our focus to be ready for Friday night."
The Cobras are fourth in the T20 Challenge series with a game in hand and still have a chance to qualify for the finals if they win their three remaining matches.
Pybus said he could not add much more information to the statement released earlier Thursday by the SA Cricketers' Association (SACA).
It confirmed that Kleinveldt, who played two T20 internationals for South Africa, would be withdrawn from the rest of the domestic competition as a precaution.
The World Anti-Doping Agency defines a "specified substance" as one that is "more susceptible to a credible, non-doping explanation."
While SACA would not name the substance, 29 year-old Kleinveldt can request the testing of a "B" sample.
"It's a due process which needs to be followed," said Pybus.
"But it's not very pleasant for Rory and he needs all the support he can get," he said.