Landlocked South Sudan had agreed to pay a pipeline transit fee of $9.48 per oil barrel to transport its crude through Sudan, a significant drop from Khartoum's initial demands of up to $36 a barrel in fees.
In addition, the country agreed to make a "one-off payment" to Khartoum of some $3 billion to cover the massive financial gap created by the South's independence last year, a fractious divorce that left a raft of issues unresolved.
"We welcome the agreement reached by Sudan and South Sudan on the issue of the allocation of oil benefits," foreign ministry spokesman Qin Gang said in a statement.
"China calls on the the two Sudans to find more political courage, cooperate with international mediation efforts, maintain the sound atmosphere and momentum for negotiation and resolve the remaining issues."
Qin further praised the role of the African Union in brokering the Saturday deal and urged Juba to resume oil production as soon as possible.
Energy-hungry China is the largest purchaser of oil from South Sudan, which proclaimed independence from Sudan in July 2012, and has had a longstanding relationship with Khartoum from which it also buys oil.
Since the two nations began slinking back toward war over the oil issues early this year, China sought to play a neutral role between both sides.
South Sudan separated with about 75 percent of the former united Sudan's oil production, but Juba still depended on the north's pipeline and Red Sea port to export its crude.
In April, South Sudan's President Salva Kiir visited Beijing and received an $8 billion loan for infrastructure development in the impoverished country.