The Indian chess star defeated the highly-rated Giri, pipping the Dutchman in the tiebreak after the four-game rapid online semifinal match ended in a 2-2 stalemate.
The win in the 15th and final round of the preliminaries late on Sunday saw the teenaged GM knock Gujrathi out of contention.
Praggu, as he is affectionately called, pulled off a massive victory over Magnus Carlsen — reigning world champ (classical) and a three-time world rapid champion.
Praggnanandhaa took fourth place with 12 points behind Duda (14 points), Vietnam's Liem Quang Le (13) and world No 1 Magnus Carlsen (12) of Norway.
Grandmaster R Praggnanandhaa has failed to qualify for the knockouts in the ongoing Airthings Masters, an online rapid chess tournament.
Praggnanandhaa was three years old when he took to the sport after his elder sister Vaishali was introduced to it to wean her away from watching too many cartoon shows on TV.
Praggnanandhaa won with black pieces in 39 moves in a Tarrasch variation game early on Feb 21 to halt Carlsen's run of three straight wins.
Gujrathi shared honours with Jan-Krzysztof Dudato take his tally to four points while Praggnanandhaa held Sam Shankland to a draw late on Friday.
Grandmaster R Praggnanandhaa is preparing in earnest for the Tata Steel India rapid chess tournament which begins in Kolkata from November 17.