Having opened their campaign with a 1-1 draw in Luxembourg last month, Belarus then fell to a 2-0 defeat at home to Ukraine in Group C on Thursday.
However, it was Saturday's 3-1 reverse against Slovakia in Borisov that proved to be the final straw after it left Belarus off the bottom of the group on goal difference.
Kondratiev took over from German Bernd Stange in 2011 but, aside from a 1-0 friendly victory over Japan 12 months ago, Belarus have failed to punch above their weight under the 54-year-old.
The Belarusian Football Federation will now begin the search for a new coach to lead them through the remainder of the campaign.
Belarus face a trip to European champions Spain on November 15 for their next qualifier.
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