Trains will be replaced by buses after around 8.30pm between Sundays and Thursdays from 4 September to 8 December, and 8 January to 31 March.
Services on some lines which use part of the route will also start later on Sundays - around 11am.
These include Perth-Dunblane-Stirling-Edinburgh trains.
The £742 million electrification project – the Edinburgh Glasgow Improvement Programme – is already running seven months behind schedule, with electric trains not now expected to start running until next July.
The Alliance warned there would be further disruption to follow, including on other routes.