Mullah Mohammad Omar also called on his fighters to intensify their insurgent campaign against Afghan and Nato forces, and urged all Afghans to boycott next year's elections, including the vote to elect a successor to president Hamid Karzai.
Violence across Afghanistan has risen as insurgents try to retake territory ahead of the full Nato pull out at the end of 2014.
The Taliban, whose tactics include roadside bombings and suicide attacks, have been blamed for the overwhelming majority of civilian casualties.
Mr Karzai and US Secretary of State John Kerry reached an agreement in principle at the weekend on the major elements of a deal that would allow American troops to stay in Afghanistan after 2014 and allow the US to lease a number of military bases around the country.
However key issues, such as immunity for American troops who will stay on, remain unresolved. The jurisdiction over those forces must still be worked out, and the US has said this was a potentially deal-breaking issue.
Mr Karzai has called tribal elders for a meeting of a consultative national assembly, known as Loya Jirga, for next month.
In his message, Mullah Omar warned members of the Loya Jirga not to approve the deal.