The club were relegated from the Bundesliga in 2010 and missed out on an immediate return to the top flight in May when they lost the promotion/relegation play-off against Borussia Monchengladbach.
Funkel's side have struggled so far this term in the 2.Bundesliga, lying second-bottom of the second tier on four points from seven games, prompting the club to take action and relieve the coach and his number two of their duties.
Jens Todt, of the club's supervisory board, told www.vfl-bochum.de: "We thank Friedhelm Funkel and Christoph John for the good work they have done in the past 15 months.
"The step is not taken lightly, especially since the relationship between the head coach and the team is intact.
"By changing the coaching staff we want to start afresh. The team has a lot of quality, but it is not currently reaching its potential."