Williamson was at his lethal best as he scored 95 runs but failed to guide his team to a win as he was removed by Shami in the final over. The Kiwis needed 9 off 6 balls and 2 off 4 but Ross Taylor could only tie the game as he dragged the ball on to his stumps in the final ball off Shami.
Williamson followed up his excellent 95 with an unbeaten 11 in the Super Over, but it just wasn't enough as Rohit Sharma and K.L. Rahul took Tim Southee to the cleaners.
"Super Overs aren't really our friends. To be honest we would have liked to get across the line earlier and not in the Super Over. It's just a shame that we couldn't get past the line," said a disappointed Williamson at the post-match press conference.
"It is pretty disappointing to be on the wrong side of the result after doing a lot of hard work. (But) There was a lot of improvement after the first two games.
"If we reflect on the match, then it was a brilliant game. India had a good total on that surface and they did well with the ball because it was taking some turn as well. The guys fought back nicely after the start India got with the bat. And we were able to build partnerships and take the game deep," he added.
Williamson took on Bumrah (0/45) but said he did not plan to go after India's best bowler.
"No, not really targeting him (Bumrah), it was just that we need 10s (per over). There are big challenges that we have seen in every game but I guess you are trying to do the best and keep up with the asking rate."
"Maybe ask AB (de Villiers) or other superstars (how to play Bumrah), but for me I was just trying to look for areas on that surface. It doesn't always come off but it was nice that we were able to get so close without quite getting across the line," he said.
The next two matches of the series will be played in Wellington and Mt Maunganui within the next four days and Williamson said the team has to keep moving forward.
"The second game in Auckland wasn't our best game, it was a tough surface and the T20 format is a game of small margins," he said.
"As we have seen throughout these and other couple of games, India's experience helped them to come through some crunch moments. But it is a game of small margins so we want to learn from this and use this experience to get better.
"Yes it was close and an emotional roller coaster. But we have to keep moving our focus forward. We know the quality of the Indian side but for us it is important to keep moving as a group," he added.