Wicketkeeper-batsman Jos Buttler stood in as skipper for the 2-1 series win against a Bangladesh side that had won their six previous ODI series at home.
“He (Morgan) will definitely be captain in India. There can’t be any way around it — he deserves it,” Farbrace told reporters in Chittagong.
Farbrace was among a number in the England hierarchy to express disappointment with Morgan and opening batsman Alex Hales’s decision to skip the tour.
The pair, however, were expected to return for India and Farbrace said he would have no concerns over their likely inclusion.
“The one-day team is particularly close. There are a lot of mates in the team,” he added.
“That helps when those who haven’t been here come back in January, because it is close-knit.”
Buttler scored 145 runs during his three matches in Bangladesh and Farbrace urged the 26-year-old to carry his fine form in ODIs into test cricket.
“The way Jos has batted out here, he has looked like he’s been batting on different pitches,” Farbrace said.
“He’s on this trip as the second keeper to start with, but if he plays that way again. There is no reason he can’t get back into the side.”