A seven-wicket defeat at the Arun Jaitley Stadium on Tuesday meant that the Proteas surrendered a 1-0 series lead to lose the three-match sequence 2-1.
The tourists were also beaten by the same margin in the T20I series against the hosts a few days earlier in the tour.
Boucher, who was leading the Proteas for the final time in a bilateral series before stepping down after the T20 World Cup, explained that there were many reasons for the poor results.
"I think it took us some time to get use to the conditions," Boucher said. "We didn't arrive early enough but there were reasons for that as well.
"The first game was pretty difficult to be judged by but I think we got better as we went on there. I think there were little moments in games, especially in the one-day format that we let ourselves down.
"In the last game we just didn't rock up. We had a few soft dismissals up front which put us under pressure, I think India bowled really well as well, they bowled with good aggression and intent, which lead to our downfall.
"Overall we do understand though, and I said it before we left, we need to try and play this series and obviously try and win."
He added: "We haven't done that but I think we've taken some good lessons and we've had some good chats behind closed doors to speak about things we can get a lot better at and I think that will stand us in good stead going forward now to Australia where conditions are completely different.
"So I just think we're okay at the moment, certainly it's disappointing to lose but we have a massive competition around the corner and that's what we're really gearing up to."
The Proteas will fly directly to Australia ahead of the T20 World Cup where they will set up base in Brisbane before their opening game of the tournament on 24 October.
Boucher felt that it had been a challenging few months for his team and getting the guys to Australia in the right frame of mind was important.
"We're coming off a long tour to England then on to India and a couple of the guys were in the Caribbean (Premier) League as well," he continued.
"We don't want to get into a situation where you're rocking up for every game and it sort of seems like a league game.
"So I think keeping the guys mentally and physically fresh is going to be vital for us management and myself to monitor. Then I think we'll get the best results for our guys being really up for the World Cup games.
"Also we're going to Australia now where I think it will suit our fast bowlers a lot better. We've got some good pace, we got some good bounce in our attack so we need to keep the pressure there."