Stefan Bredohl told a regular government news conference that it was "crucial" for the West to have a partner in Islamabad who contributed to regional peace and development.
"We expect that we will continue to deal with a Pakistan government (and) with a Pakistani president in the future who does not only have an eye on the situation in Pakistan itself but also on regional stability and who does his part to contribute to peace and stability in Afghanistan," he said. "Peaceful conflict resolution with its neighbours and decisiveness in fighting terrorism in all its forms are of crucial importance to us."
Bredohl said Berlin would support an effective Pakistani leader who fostered democracy and the rule of law. "The German government hopes that the democratic government in Pakistan and also the future president will now seize the opportunity to bolster the democratic institutions in Pakistan and address the urgent challenges facing the country," he said.
"Germany will continue to stand by Pakistan in the future as the country develops and stabilises its democracy."
Germany has some 3,500 troops stationed in northern Afghanistan with the NATO-led International Security Assistance Force. Relations between Musharraf and Afghan President Hamid Karzai have been tense over a surge in Islamic extremist violence affecting both countries.
Karzai has repeatedly accused Pakistan's intelligence services of supporting a Taliban-led insurgency against his administration and Afghan officials have accused Islamabad of not doing enough to clamp down on militant sanctuaries.