Supporters of the plan also argued there were clear educational benefits for students if they started the school day later.
But the move, backed by the socialist SP party, was voted down by 107 to 63 votes with opponents lining up to criticize the proposal.
The centre-right FDP party said surveys showed students didn't want to start school later and argued the proposed move would have cut into after-school sport and leisure activities.
The conservative BDP party also voted against the move, arguing school children need to get used to the sort of hours they will be keeping when they become employees.
The Greens weren't on board with the plan either, arguing it wouldn't help ease the squeeze on public transport.
In fact, the move threatened to put more pressure on Zurich's public transport in the late afternoon, the Greens argued.
The party made the argument despite backers of the plan saying the later start to the school day would be compensated for by a shorter midday break rather than longer hours in the afternoon.
Supporters of the move had hoped to convince opposition parties of the educational benefits for children of starting school half an hour later, with one backer saying it would help “optimize biorhythms”, but the arguments fell on deaf ears.
The decision in Zurich comes in the wake of the failure of a similar initiative in the canton of St Gallen in February. Meanwhile, a survey carried out in Bern in 2015 showed 81 percent of students did not wish to start school later.
By contrast, a high school in Alsdorf in Germany has this year become the first in that country to allow pupils to decide whether to start at 8am or 9am.
The Alsdorf scheme would help combat the problem of "social jet lag" and lead to fewer sleepy students in class, one expert told Swiss daily the Tages Anzeiger.