Sheikh Tamim bin Hamad Al-Thani's two-day visit to Indonesia, Southeast Asia's largest economy and the world's most populous Muslim country, comes amid heightened Gulf tensions.
Saudi Arabia, the United Arab Emirates, Bahrain and Egypt severed ties with Qatar on June 5 over its alleged support of extremism, charges Doha denies.
Talks focussed on investment and trade opportunities in energy, infrastructure and tourism.
But the emir said the two leaders also discussed the "unjust siege" of his country by neighbouring Gulf states.
More From This Section
Al-Thani led a delegation of 40 businessmen who also accompanied him to Malaysia and Singapore.
"This is a very important visit and the first visit for emir Al Thani to Indonesia which also coincides with the commemoration of 41 years of diplomatic relations between Indonesia and Qatar," Widodo told reporters after closed door talks.