The BFU had ruled on Monday that CSKA should play their next three home matches at a neutral ground and pay a fine of 15,000 levs ($10,370) for the riot in the northwestern town of Mezdra.
The sanctions were imposed after more than 100 CSKA fans stormed the field a few minutes after striker Ismail Isa put Lokomotiv in front midway through the second half, forcing referee Ivaylo Stoyanov to abandon the game.
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The BFU's sports and technical commission awarded Lokomotiv a 4-0 victory. The Mezdra-based club were leading 1-0 when the match was abandoned in the 65th minute.
"This is our final decision," commission spokesman Hristo Botev told reporters, adding that CSKA had no right to appeal.
The decision leaves CSKA second in the standings with 38 points from 19 matches, four points behind leaders Litex Lovech.
The 31-times Bulgarian champions will begin their stadium ban on Wednesday.
BFU vice president Yordan Leckov and the Professional Football League's President Valentin Mihov had been keen for the season to be suspended.
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