The win in the 15th and final round of the preliminaries late on Sunday saw the teenaged GM knock Gujrathi out of contention.
R Praggnanandhaa pulled off a win over compatriot Vidit Santhosh Gujrathi in a marathon 10th round clash at the Tata Steel Masters chess tournament.
Gujrathi shared honours with Jan-Krzysztof Dudato take his tally to four points while Praggnanandhaa held Sam Shankland to a draw late on Friday.
Humpy scored 11.5 points from 17 rounds to take fifth place after finishing equal on points with two others. A loss to Polina Shuvalova in the final round hurt Humpy's chances of a better finish.