The surprise triumph sees the Indian shuttler move through to a second round clash against the formidable Kento Momota, the current world number one.
In the opening exchanges, neither player was too aggressive but Prannoy raced to an 11-4 lead with his superior drop shots and winners.
His confidence only rose after the mid-game break as he kept attacking Tsuneyama. The Japanese shuttler had no answer to the barrage of smashes and lost the game in quick time.
The world No.10 did not surrender in the second game though. He learnt from his previously defensive approach and started to attack more often but Prannoy matched him point-for-point on many occasions.
Prannoy, who has had a poor season in 2019, was efficient with his play as he calmly dealt with everything that Tsuneyama threw at him, ensuring that he stayed a step ahead of the higher-ranked Japanese.
Though Prannoy did not completely dominate the second game, he did more than enough to close the match and progress to the next round.
Sameer Verma prevails over Wangcharoen
Sameer Verma ensured a happy end to the day for Indian fans as he won 21-16, 21-15 against Thai No.11, Kantaphon Wangcharoen.
The tie started off closely with both players tied at 8-all at one point before Verma, who is ranked 33rd, went into the interval with a narrow 11-9 lead. Wangcharoen won a few quick points but Verma consistently maintained the upper hand to comfortably take the first game.
The consequent game followed a similar script and ended with Verma easing into the second round, where he will face off against local favourite, Lee Zii Jia.