Rovers' 4-1 defeat to Limerick marked the end of Croly's reign in Tallaght.
Croly had been in charge since November 2012 and secured three trophies in his time in charge of the Dublin club - the Setanta Sports Cup, the League of Ireland Cup and the Leinster Senior Cup.
Rovers currently sit fourth in the Airtricity League Premier Division, a full 12 points behind leaders Dundalk.
Assistant manager John Gill will take charge of the club while a permanent successor to Croly is being sought.
In a statement released on their website, the club stated: "Trevor has worked hard for Shamrock Rovers and secured three trophies during his spell as manager.
"He has also created strong football structures which will benefit the club into the future.
"We would like to wish Trevor the very best for the future."
