The championships concluded in Bengaluru late on Saturday and the results were declared on Sunday.
Shahan will now represent India in the Grand Finale at Sarno, Italy, from October 19 to 26. He will compete with 350 drivers from over 60 countries.
Speaking to on way to Agra from Bengaluru, Shahan said he was excited at having won in this category.
"It was pretty amazing," he said.
He practiced very hard for many years in Bengaluru. A student of Delhi Public School (DPS), Agra, Shahan now returns to the city with laurels.
Last week, woman cricketer Poonam Yadav brought cheer to Agra's sporting fraternity after being nominated for the prestigious Arjuna Award.
Shahan's father Shahroo Mohsin told that the championships concluded late on Saturday and the results were declared on Sunday.
"Following a mixed Round 2 in the MRF F1600 Championship, where Shahan encountered rain for the first time in his single-seater career, he was back to his karting roots this weekend for the final round of the 2019 JK Tyre FMSCI National Rotax Championship.
"With a 12-point advantage in the senior category, Shahan entered the weekend with confidence along with his team MSport. Like in the other rounds, Bengaluru's Meco Kartopia hosted the finals, where new champions were to be crowned in the Micro Max, Junior and Senior categories," he added.
Last year, at the age of 14, Shahan became the youngest to compete in the senior category in India. This helped him to be crowned the youngest Indian national karting champion in the senior category.
Mohsin clarified that Shahan had been allowed to compete as per the guidelines set by the Federation Internationale de l'Automobile (FIA) and Central Index Key (CIK), especially with regards to the age limit.
Shahan finished the third round in very wet and tricky conditions and was second in the final. This was enough, though, for Shahan to seal the title, his sixth championship win in four years.
The senior title adds to his 2015 Indian National Cadets, 2016 Asian Cadets, 2016 Indian National Cadets, 2018 Indian National Junior and 2018 Indian Junior X30 series titles.
"First of all, it was a big relief to get over the line. Even though I had a handy lead, still one needs to finish the weekend. One technical error and it can snatch away all your points," Shahan said.
"It was a day of mixed weather as it started out dry but the two races in the end were under tricky conditions, with the final being a crazy race where we were running the slick tyres in wet conditions.
"It was all about bringing the kart home with enough points to seal the championship. A big thanks to my team MSport and JK Tyre without whom, this wasn't possible," he added.
( With inputs from IANS )