Only two astonishing misses by substitute Angelo Henriquez spared the Serbians from a heavier defeat, with centre back Guillermo Maripan heading in an 89th-winner for Chile who failed to qualify for the 32-nation tournament.
Krstajic fielded an experimental 4-2-3-1 formation which failed to spark as their final pass kept going astray and the defence looked shaky every time the South American side came forward purposefully.
Right back Antonio Rukavina looked particularly vulnerable and striker Aleksandar Mitrovic was ineffective with Serbia's build-up slow and predictable.
Talented winger Nemanja Radonjic looked the only Serbian threat as he came close twice with shots from the edge of the penalty area while Chile missed a string of chances at the other end.
Serbia keeper Vladimir Stojkovic produced two fine saves to deny Felipe Mora and Diego Valdes before man of the match Junior Fernandes, who gave his markers a torrid time on either flank, set up a pair of sitters for Henriquez.
The former Manchester United prospect missed a gaping goal from three metres in the 75th minute and shot wide with only Stojkovic to beat.
The Chileans were rewarded in the dying minutes for their more adventurous approach after Maripan rose above his marker to head home an inswinging Jose Bizama cross from the left.
Serbia will play their final warm-up game against Bolivia, also in Graz, on Saturday before flying to Russia where they face Costa Rica, Switzerland and Brazil in Group E.
(Writing by Zoran Milosavljevic in Belgrade, editing by Ed Osmond)
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