Raina, who was brought back into the ODI side after a gap of one year, had also missed the first one-dayer at Dharamsala.
The BCCI Medical team today confirmed that Raina was ruled out of the second ODI, which is scheduled to be held here on Thursday, as he was still not match fit.
"The team management has allowed Suresh Raina more time to recover. There will be no replacement in the team," a BCCI release said.
Raina batted for about 45 minutes at the nets today but the Indian team management confirmed that he was still not 100 per cent match fit to play in the second game of the five-ODI series.
29-year-old has been looking forward to featuring in his first ODI since October 2015. The southpaw was dropped for the ODIs in Australia and the limited-overs tour of Zimbabwe earlier this year besides the two-match T20 series against the West Indies in USA.
He has not had time in the middle since the Duleep Trophy where his scores read 52, 35 and 90.
Raina led Uttar Pradesh in the team's Ranji Trophy opener against Madhya Pradesh but did not come out to bat. Uttar Pradesh suffered an innings and 64-run defeat at the hands of Madhya Pradesh.
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