The Pune franchise was bought by Kolkata-based business tycoon Sanjiv Goenka's company New Rising, while the Rajkot bid was won by Intex Mobiles.
While Goenka will shell out Rs 10 crore per year to the BCCI, Intex Mobiles will pay Rs 16 crore for the two-year deal.
"They won't take a single penny from the BCCI. In fact they will pay the BCCI," Board Secretary Anurag Thakur told reporters after a meeting of the IPL Governing Council here.
The teams were sold through the reverse bidding process for which the base price was set at Rs 40 crore and bidders had to quote an amount less than that. The lowest bidder was given the franchises.
However, both the CSK and RR will be allowed back in the league after serving out their suspension.
The interim franchises, which have been picked today, will be allowed to participate in a draft to first retain their share of players.
Rajkot and Pune will have draft picks on December 15 and Pune will get to pick the players first.
The cricketers who remain unselected will go to general pool to be available for fresh auction, scheduled for February 6 in Bengaluru.
Both the CSK and RR will be allowed back in the league after serving out their suspension.
The BCCI also announced that the Franchise workshop will be held in Srinagar on January 13 and 14.
Players from CSK and RR will be divided into two groups of capped and uncapped and the top names will be sold through the draft system. The two new teams will have a minimum of Rs 40 crore and a maximum of Rs 66 crore to buy their players.
The two teams were earlier disqualified from participation for two years owing to match-fixing allegations.
IPL 2016 will be played from 9th April to 29th May and player auction will be held in Bangalore on February 6.