From 2014, stewards will, for example, be able to hand out five or 10 second penalties, which will be taken at a driver's subsequent pitstop.
If the driver does not stop again, then the penalty will be added to their race time.
The new system has been proposed to ensure drivers are not punished by a hefty drive-through for a minor infringement.
It was agreed during a meeting of F1's Sporting Working Group in Singapore this weekend and will now be put to the FIA World Council for approval.
Teams have also agreed that Pirelli can tweak the front and rear tyre compounds next season to balance out the car demands of the new 2014 engine regulations.
There will still be only four compounds available for the season - super-soft, soft, medium and hard - but within each of those the front and rears no longer needs to be identical as is currently mandatory.
The new turbo engines are set to deliver more torque over the current V8 power units, which will put a heavier demand on the rear tyres.
Further matters that were approved include tighter pitstop safety rules, which include mandatory over-ride facilities for pit crews, and the ratification of penalties for unsafe pitstop releases.
The exact details of the changes are set to be confirmed following the FIA's WMSC meeting next week.