The 36-year-old was handed the job on a full-time basis last December after leading Basle to a surprise win over Manchester United in the Champions League during a spell as interim coach.
Basle also went on to lift the domestic Super League title, their third in a row, but this season has not gone as well and they currently lie eight points behind leaders Grasshoppers in the league table, leading to Vogel's departure.
Former Lucerne boss Murat Yakin has been appointed their new coach, a statement on Basle's official website confirmed.
"Heiko Vogel's premature release from his current contract was the result of an assessment of the actual state and sporting development of the first team," it read.
"Different views over the further development of our cooperation, the unsatisfactory start to the season and the failure to raise the team led to the current assessment.
"No common ground could be found, which is why the board had to consider a termination of cooperation as the obvious solution."
Yakin has signed a contract until June 30, 2014.