After losing Sunday's Royal London ODI opener, England needed to triumph on Wednesday to take the three-game contest to a decider at Lord's this weekend.
But Jones' side slipped to an 88-run loss following Kaur's devastating spell, which included 18 fours and four sixes and ended with her hitting 43 off her final 11 balls.
"Every loss is tough, but Harmanpreet batted brilliantly," said England captain Jones. "It was almost like she flicked a switch, and really took it to us at the end. We struggled to defend. It was difficult.
"It was important to slow her down as much as possible, and while our bowlers are exciting and young talents, they are inexperienced.
"Everyone knows inexperience can bring inconsistencies, and while we have seen some great spells in this series and during the summer, coming up against such a good batter in such good form was always going to be a challenge.
"It will be great learnings for them, and us a whole group, as to how we respond to moments like that.
"Reflecting on what is a good ball and what is a good shot in the moment is important, because it just felt like everywhere we bowled she was finding the boundary."
Responding to India's 333, the home side slipped to 12 for two and then 47 for three, and although Danni Wyatt provided some hope with 65, the hosts were dismissed for 245 as India celebrated winning their first series on English soil in 23 years.
Jones, who scored 39 runs, added: "We didn't get close enough. We lacked partnerships and we needed a match-winning innings, too.
"But there are points on the line at Lord's on Saturday. It will be a quick turnaround and it is a great opportunity for a younger side to step up and show what we can do.
"It's been a long season and it'd be brilliant for us all to be in that changing room at the end having won the game."