From the last ODI series India played - against England at home in January - Amit Mishra was dropped for Shami and Rohit back to open the innings with KL Rahul ruled out of the tournament as he recovers from shoulder surgery.
Pace spearhead Shami and batsman Rohit Sharma are the only changes from the team that played England in three one-day internationals this year.
Gambhir's loyal fans also slammed the Indian board and a hashtag named #bringbackgambhir was soon trending on social micro-blogging site Twitter.
The BCCI board have unanimously voted to participate in the 2017 Champions Trophy despite a dispute with the ICC over revenue shares.
India will take on Pakistan, South Africa and Sri Lanka in Group B. India won in Pune and Cuttack but lost in Kolkata. R Ashwin, who is now recovering from a sports hernia, and Ravindra Jadeja can perhaps expect part-time assistance from Yuvraj Singh, who kept his spot after his ODI career was given a re-start in the series against England in January.
Several members of the Board Of Control For Cricket In India (BCCI) favoured withdrawing from the tournament in protest but court-appointed administrators, who are now supervising BCCI operations, rallied against such a drastic move.
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Yesterday, the BCCI ended all speculation on India's participation in the next month's Champions Trophy saying that that the Men in Blue will play the 50-over pinnacle event.
Former captain Mahendra Singh Dhoni retained his place in the squad amid whispers that the wicketkeeper-batsman's "finisher" reputation was on the wane. "He narrowly missed out", Prasad explained after the selection committee meeting here.
The BCCI delayed naming the Indian team because of its objections that a new ICC financial formula hurts India's interests by reducing its revenues from $570 million to $293 million for the period 2016-23.
Skipper Virat Kohli comes in at No 3 slot. The swashbuckling all-rounder is also in the squad for ICC Champions Trophy 2017.
He also expressed his views on a player being picked in an ODI side based on IPL performances.
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