In a joint statement issued after the meeting both sides promised to build their future on “mutual respect”.
Relations have deteriorated sharply since Damascus ended its three-decade military presence in Lebanon in April.
Anti-Syrian parties then won a parliamentary majority in elections in May and June.
“We undertook to work to build Syrian-Lebanese relations based on mutual respect and to distance anything that could damage these privileged relations,” said the statement following talks between Mr Siniora and Syrian premier Mohammad Naji Otari.
Mr Siniora’s trip comes just a day after his government won parliamentary approval, drawing a line under a tortuous process that led to the formation of his cabinet.
The two sides also announced the lifting of an effective road block at the Syrian border that has held up thousands of goods trucks trying to leave Lebanon in recent weeks.
Following his meeting with Mr Otari, Mr Siniora headed for talks with Syrian President Bashar al-Assad.
Mr Siniora later told journalists that Beirut would work to find a solution to “all the problems currently on hold”.
Mr Otari said that during the talks “all matters of interest between Syria and Lebanon were examined as well adequate mechanisms that will be aimed at eliminating all obstacles preventing their development”.
The Syrian premier said that joint committees for defence, security, foreign and economic affairs “will be activated” alongside a joint commission to look into Syrian and Lebanese “disappeared”.
The Syrian government daily Tishrin said that Damascus would pass on “requests from families” of 795 Syrians reported missing in Lebanon, a matter that was never officially discussed between the two in the past.
Relatives of hundreds of Lebanese who disappeared or were imprisoned while the country was under the Syrian yoke also want news on the fate of their loved ones.
Syria’s pullout three months ago was sparked by intense international pressure in the wake of the killing of former Lebanese premier Rafiq Hariri.
In June, an anti-Syrian Lebanese politician and journalist were killed in separate bomb blasts in Lebanon, leading the Lebanese opposition to again point the finger at Damascus for their deaths. Syria has denied any involvement.