On a dramatic last day when hot contender Peter Whiteford of Scotland was disqualified for a moved ball in the third round, Kruger carded four birdies and a bogey in a final-round three-under par 69.
The 25-year-old from Bloemfontein finished on 14-under 274, two strokes ahead of Spaniard Jorge Campillo and Marcel Siem of Germany, after just three shots had separated the top 15 at the start of the day.
Jose Manual Lara of Spain and Australia's Marcus Fraser came in third at 11-under in an absorbing finale at the par-72 DLF Golf and Country Club on the outskirts of New Delhi.
Whiteford, who led the first two rounds and was one stroke behind leader Kruger after the third, was penalised for the moved ball on the 18th fairway during his round on Saturday.
The Scot was disqualified after the rules committee reviewed the incident on Sunday morning, following television viewers alerting chief referee John Paramor about it.