Khanna, the All India Tennis Association (AITA) President, lost the ITF Presidential election by only eight votes to American candidate David Haggerty but has become the first Asian to be elected Vice President.
Khanna managed 192 votes to 200 by Haggerty in a close second round, while two other candidates -- Juan Margets (Spain) and Rene Stammbach (Switzerland) -- were eliminated in the first round.
The new 13-member Board then elected Khanna as the new ITF Vice President.
"I am grateful to the nations who were a majority in number present for the AGM. I am grateful for majority nations for voting for me, although it reflected differently because of weighted voting pattern for election. I am thankful for election to the board and now vice president," Khanna told PTI.
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"I will do my bit for bringing the change in ITF for the main stakeholders, the lower-ranked players and the National Federations who are spending money on development without much help from the bodies making profit out of our sport," he added.
According to the Sports Ministry, the Indian administrator's election as AITA President is in violation to the Sports Code.
Khanna has always been critical of the way the current ATP set up works, saying it was heavily loaded in favour of only top-100 players, who are mostly from Europe.
Khanna is also President of Asian Tennis Federation (ATF) but his efforts to begin a closed circuit for the Asian players did not yield desired results.
The AGM also approved introduction of fifth-set tie break in the Davis Cup matches.