Instead they are backing original proposals to build it in another area of Newton Mearns.
The plan to position the mosque at Eastwood High School sparked an opposition campaign, with parents complaining about the facility being built on the site, which they say is earmarked for a second playing field at Eastwood High.
Yesterday, the council decided to revert to the original plans to build on a site in the town's Maidenhill area.
They have promised to ensure a suitable mosque site for the Muslim community as the town currently has no permanent place of worship
Consultation by East Renfrewshire Council over the plans attracted thousands of responses - a total of 2916 people shared their views with 1921 objecting, while 995 lent their support.
A council report recommended the proposals be dropped following the consultation and a meeting of the full council was held.
The council's depute leader Tony Buchanan proposed the move, which was seconded by council leader Jim Fletcher.
A spokeswoman for East Renfrewshire Council said: "This decision follows extensive consultation with the local community over a six-week period.
"The council has now agreed to revert to its original plan, which proposed a site in the Maidenhill / Malletsheugh area of Newton Mearns as suitable for a mosque.
"This is in line with what local people have expressed a preference for and we will progress with the proposal to ensure a suitable mosque site for the Muslim community of East Renfrewshire."
Meanwhile, plans to move a new denominational school from the Maidenhill area to a site in South Waterfoot Road, has been agreed.
The overall plan will now go to the Scottish Government Reporter for final approval.