The 22-year-old Assamese, who is a World Championship bronze-medallist, went down 0-3 to Thailand's Chatchai Butdee in the summit clash. Butdee is the reigning Asian champion.
Shiva had booked his ticket to Rio de Janeiro by making the finals yesterday after beating Kazakhstan's Kairat Yeraliyev.
Meanwhile, it was a heartbreak once again for L Devendro Singh (49kg), who missed a second opportunity to qualify for the Olympics.
The Commonwealth silver-medallist, who lost in the semifinals yesterday, today went down in the box-off for the Olympic slot.
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However, that was not enough to make up for the deficit he conceded earlier in the bout.
Tomorrow, star woman boxer M C Mary Kom (51kg) will take on Chinese Taipei's Yu-Ting Lin in the box-off to decide the new rankings and seedings for next month's World Championships in Kazakhstan.
Mary Kom had missed out on an Olympic quota place after losing the semifinals of the ongoing event yesterday. In the women's draw, this tournament offered Olympic berths for only the gold and silver-medallists.