Root missed the last ODI in Kolkata, where England recorded a narrow five-run victory, with a groin niggle but is fit enough to retake his place at No.3.
“Joe has recovered really well, it was just a niggle and a risk we didn’t feel we needed to take given it was a bit of a dead rubber,” said Morgan.
“It was also a good opportunity for the guys who’ve sat on the sideline to show the form they’re in. Joe is fit for this game.”
Root’s Yorkshire teammate, David Willey, misses out with a shoulder injury.
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“David flew in yesterday, missed practice in the morning and he won’t be fit for selection,” Morgan added.
“Nothing serious showed up on the scan, which is a huge positive because initially it looked quite painful, but he won’t be fit.”
England may be moving on from 50-over cricket to Twenty20 in Kanpur but captain Morgan still has his eyes on the prize that is the Champions Trophy.
The primary focus of the national side for the first half of the year is coming out victorious on home soil when the world's top eight one-day international sides do battle in June.
That makes a three-match T20 series to conclude the tour of India slightly incongruous but it is hardly the most worrying or egregious quirk of the sport's baffling calendar.
And Morgan, for one, believes the games can still be important preparation for the Champions Trophy as methods, tactics and personnel increasingly leach between the limited-overs formats.
Only two members of the T20 squad - pace pair Tymal Mills and Chris Jordan - were not part of the one-day group and England's preferred aggressive style now differs little whenever a white-ball is involved.
"What we're seeing now is your 50-over team is almost identical to your T20 team. The same risk level and skill level you have to show in both forms is pretty evident," said Morgan.
"Around the 2015 World Cup you might have had three or four changes between the two groups. You might have had specialist T20 players coming in but we only really have one or two now.
"Fifty-over and 20-over cricket are similar and probably (getting) more alike. It will happen naturally but the difference will be between being a Test player and a white-ball player.
"Going from the series we've just played where bowlers have found it difficult, honing your specific skills into T20 cricket can be relevant."