The Czechs, however, can reclaim outright first place by beating Latvia later in the day.
Bolton Wanderers forward Gudjohnsen, back in the side for the first time since going back on his November 2013 decision to retire from international football, gave Iceland the lead in the 20th minute.
The former Barcelona and Chelsea marksman received a pass from Johann Gudmundsson and the 36-year-old slid the ball into the corner of the net to notch his 25th goal for his country and his first since 2009.
Bjarnason headed the second from a cross by Gylfi Sigurdsson 12 minutes later and the same player then completed the scoring in stoppage time when his shot went in after taking a big deflection.
Iceland now have 12 points from five games while Kazakhstan are rooted to the bottom of the group with one.
(Reporting by Dmitriy Rogovitskiy, editing by Tony Jimenez)
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