The game looked to be heading for a goalless draw when Robert Akaruye scored in the 85th minute before Alisher Halikov fired home in stoppage time to secure a point.
The result means Busaiteen remain top of the standings with seven points while Neftchi have four.
Neftchi attacked from the outset at the packed Fergana stadium but were unable to turn their chances into goals.
Just as it appeared neither side would be able to make the breakthrough Akaruye fired home a free-kick with just five minutes left on the clock.
It seemed Busaiteen were all set to take all three points and extend their lead at the top of the table but Halikov grabbed his second goal in the AFC Cup campaign as the match entered injury time to earn a point for the home side.