Voluntary organisations bidding for public contracts are to be treated in the same way as commercial companies in a beefed-up version of the Compact called Compact Plus.
There will also be a Compact Champion to support bodies joining Compact Plus and adjudicate on breaches, with powers of expulsion.
The capacity-building Changeup programme will also have a different footing, with control by an independently recruited board called Capacity Builders instead of the Home Office.
The moves follow complaints of poor performance under the Compact - guidelines for contracting and funding relations dating from 1998 - and doubts and in-fighting over Changeup.
Clarke also announced investment of £70m over two years from March next year for Changeup, including the national expertise 'hubs', and £90m for Futurebuilders, which invests in service-providing voluntary agencies and is the model for Capacity Builders.
There will be a public recruitment process for a Capacity Builders board of around 10 people. Sector umbrella bodies and potential beneficiaries will be barred.
NCVO chief executive Stuart Etherington welcomed the two-year funding for the hubs and Government recognition that Changeup would still be "owned and led by the sector". Compact Plus, he said, was an "exciting new tool".
Stephen Bubb, of chief executives body Acevo, said Compact Plus offered a route to full implementation of Acevo's Surer Funding framework. Capacity Builders would address the absence of a central body to make strategy and spending decisions.
Charities minister Fiona Mactaggart said Compact Plus would ensure stable funding and reduced paperwork: "A more focused, sector-led Changeup programme will accelerate progress towards a robust support structure, helping voluntary organisations do what they do best," she said.