Emslie said Kallis' IPL contract obligated him to play for RCB in the CLT20 which begins in Johannesburg on September 16.
"Kallis' contract (with RCB) says if his IPL team get into the CLT20 his team has the first option. He is obligated to play for RCB. For that we got USD 200,000. We would have wanted Kallis but the decision did not lay in our hands. We never had a choice," he said in a media interaction with a group of Indian journalists.
"One can argue the merits of the case but that is the rule. They (CLT20) may be thinking of changing the rule in future," he added.
CLT20 rules seemed confusing after Governing Council Member Dean Kino's statement after the launch of the tournament in Johannesburg suggests that Kallis, New Zealander Ross Taylor and Australian Cameron White had the option not to choose RCB.
"CLT20 regulations stipulate that with Jacques Kallis, Ross Taylor and Cameron White playing for their IPL franchise instead of their home teams, RCB must compensate the Warriors, Central Stags and Victorian Bushrangers USD 200,000 each respectively," Kino had said.
Warriors coach Russell Domingo was also clear that Kallis had no choice but to play for RCB.
"I am under correction. But I think Kallis' contract (with RCB) says that should RCB qualify for the CLT20 they have the first call on him. We might think it is crazy, he is a South African and his club Warriors is in the CLT20 but still he is playing for RCB but that's it," he said.
"We don't pay big money, we can't compete with IPL teams. IPL dollars are going to get the first call. Money talks," he quipped.
Russell, however, said it was not a bad deal to lose out on Kallis as the Warriors are getting a lot of money in return.
"It is a big attraction to get that money. It is not a bad deal as it was out of our control to get Kallis in our side. I think we can have another player like Kallis in future (to get big money)," he said in a lighter vein.
He conceded that Kallis' absence would be a big blow to his side's chances in the CLT20 but said it was good as younger players will get a chance to play.
"It is a big blow for us that Kallis will not be with the side as he is a three-in-one player. He is one of the best batsmen, a useful bowler and very good fielder.
"But we always knew that Kallis will not be there. It gives a chance to youngsters like Collin Ingram. Kallis also did not play in some big matches last season but we still won domestic titles. We won the MTN domestic championship and Standard Bank Pro20 title without him," he added.
Emslie feels that young South African players have a big opportunity to impress in CLT20 to get a place in IPL teams.
"Blokes here have a chance to be in an IPL team if they do well in the CLT20. Though I would want my players not to get too excited about the auction," he said.
Up and coming pacer Lonwabe Tsotsobe is one such player waiting for the CLT20 as a vehicle for the IPL.
"I am waiting for the CLT20 to come. I hope I get to play in the IPL and for that I have to come up with a good performance in the CLT20 as the IPL auctions are coming up shortly after the CLT20," he said.
"My agent said I will be there in the list of players to be auctioned for the the IPL. It (IPL) is a big platform as you will get to play against the best players in the world," he added.