Changes made in the horse-trading with the opposition parties to secure its passage saw £7M cut from specialist investment programmes.
Finance Secretary John Swinney cut £4M from the transport strategy and innovation budget for 2008/9, down from £9.7M to £5.7M.
The Transport Strategy and Innovation budget funds experimental pilot schemes looking at issues such as road safety and signage.
Swinney used the money cut from its budget to hold down bus fares costs during a period of high fuel prices.
The Motorway and Trunk Roads Network Strengthening and Improvements budget was also sliced by £3M to £38M.
This will not impact on major schemes but will affect the Intelligent Transport Systems five year action plan.
This scheme is rolling out traffic control systems across Scotland, so the cut in funding is likely to slow the delivery to a six-year timescale.