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Rayudu's presence could well mean that he will replace an out-of-form Murali Vijay at the top alongside Shane Watson.
Fleming also rued the missing of some key players that he said has affected the team combination.
The five-wicket win also ended Chennai's five-match losing streak against the defending champions.
All-rounder Vijay Shankar was preferred over the 33-year-old Rayudu for the contentious number four spot in India's World Cup squad.
With the ongoing IPL the only form of cricket left before Kohli's team embarks on their World Cup campaign, the selectors maybe forced to consider the form of the players in the T20 tournament before picking the squad ahead of the April 23 deadline.
Rayudu created a frenzy by tweeting that he plans to buy 3D glasses to watch the showpiece. The 3D reference came a day after chairman of selectors M S K Prasad cited Shankar's "three-dimensional qualities" to justify his selection.
Pant and Rayudu's exclusion from the squad of 15 had created quite a stir on Monday. While Sunil Gavaskar called Pant's omission surprising, the snub to Rayudu was questioned by Gautam Gambhir.
Rayudu's sarcasm-laden '3D tweet' might have hastened his international retirement but the chairman of selectors defended the recently-retired Hyderabadi's non-exclusion, asserting that his panel cannot be accused of bias.
The 33-year-old Andhra batsman was in the official standbys list for the big event in UK, but was ignored despite injuries to opener Shikhar Dhawan and all-rounder Vijay Shankar.
Rayudu was not included in the 15-member India squad for the ongoing World Cup and despite being named in the reserves.
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