The Czechs finished third in Group B with 15 points, followed by Bulgaria on 13.
Bulgaria, who have not reached the World Cup finals since 1998, enjoyed more possession but the Czechs created more scoring chances after picking holes in the home team's porous defence.
Only a great save by Vladislav Stoyanov from Petr Iracek's close-range effort stopped the hosts falling behind after 27 minutes and tall Libor Kozak hit the post with a header just before the interval.
The home side started the second half brightly and Czech keeper Petr Cech produced a great save to parry substitute Dimitar Rangelov's curling shot from the edge of the area and Stanislav Manolev headed just wide.
But the Bulgarians found themselves 1-0 down in the 52nd minute when Dockal hit the target with a 20-metre shot as keeper Stoyanov should have done better.
Defender Petar Zanev was sent off for a second yellow card 15 minutes from time, Bulgaria's fifth dismissal of the qualifying campaign.
(Reporting by Angel Krasimirov, editing by Justin Palmer)
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