Hecking had been in charge at the Volkswagen Arena since 2012 but paid the price for a dreadful start to the season which sees Die Wolfe down in 14th place in the Bundesliga standings, with just six points from seven games played.
They have won only one league match and scored just four goals after finishing eighth in the table last term.
Villas-Boas is the man whose name has been mentioned as a possible successor, with the Portuguese tactician currently out of work having left Zenit Saint Petersburg in the summer after two years at the helm.
Hecking took training on Monday morning but was relieved of his duties later in the day, and sports director Klaus Allofs admitted it was a tough decision to have to take.
“After the last few disappointing results we took the decision to give the team new impulses through a change of coaching staff,” he said in a statement.
“On a personal level I feel sorry for this decision. In these intense almost four years we worked very successfully together.”
Southampton have announced plans for a two-week tour of China as part of their pre-season preparations for the 2018-19 season.