His first season back in club management proved a trial for the 43-year-old Dutch coach who began his career at Ajax Cape Town.
Stekelenburg left the club at the bottom of the standings with two wins and four draws from 15 matches.
Stekelenburg was Ajax Cape Town coach for just over a season, taking over from Foppe de Haan in 2011.
He had promised Ajax a top-five finish in his first year in charge but the side slumped out of the top eight and finished ninth.
When Ajax won only once in their first six games of the new League season, and were humiliated at home in a 1-5 defeat by AmaTuks, Stekelenburg was shown the door in September 2012 .
He had first moved to South Africa in 2009 as Ajax Cape Town’s head of youth.
In 2013 he went back to the Netherlands completing his top professional coach’s license and then became the under-17 coach of the Netherlands, who he took to second place at the European Championships.
Stekelenburg has been replaced at Almere City by Jack de Gier.