Fernandes, whose side had slipped to 14th and third from bottom in the league, is the second coach to leave a club inside a week after Leonardo Jardim quit Beira-Mar on Monday.
Despite Beira-Mar sitting 10th in the 16-team division, Jardim handed in his resignation after his side were beaten at home by bottom side Portimonense.
Sporting Lisbon announced last week that their coach Paulo Sergio would be relieved of his duties due to their recent struggles. Sporting sit third with 33 points but have a 26-point deficit to leaders FC Porto.
Since the start of the season four other clubs- Academica, Maritimo, Naval and Portimonense- have changed coaches. Naval and Academica are already on their third coach this season.
Fernandes is ninth coaching casualty in Portugal
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