"China will continue to view its relations with Pakistan from a strategic and long-term perspective and work together with Pakistan to elevate the China-Pakistan strategic partnership to a new high," the statement said.
Hu's visit to Pakistan is the first by a Chinese leader in a decade.
Trade agreement
The two sides also hailed the Free Trade Agreement signed on Friday, saying it would serve as an "engine for balanced growth of volume of trade" between the two countries.
The deal is expected to triple bilateral trade to more than US$15 billion over the next five years.
China also offered Pakistan help with its energy and mining industries.
The two countries vowed to jointly combat terrorism, separatism and extremism, saying those "three forces" posed great threats to regional peace, stability and security.
Nuclear ties
Hu said on Friday after talks with Musharraf that Beijing would carry on cooperating with the nuclear power industry in Pakistan.
China has already built one reactor and is helping to construct another. However, he did not announce any new deals.
Beijing remains Islamabad's largest arms supplier, and the two are jointly developing the JF-17 Thunder fighter aircraft. China has also invested millions of dollars in a deep sea port in southwest Pakistan to access the Arabian Sea.
Hu's visit to Pakistan followed a trip to its South Asian rival, India.
He is scheduled to return to Beijing midway through Sunday after inaugurating an economic zone.