Foreign Minister Nasser Joudeh told state news agency Petra that Ambassador Bahjat Suleiman had violated diplomatic protocol.
"The Syrian ambassador has breached all norms and diplomatic practices by his behavior ... This is considered as a final warning to abide by the rules of diplomatic practice and to stop any meetings or statements that are deemed harmful to Jordan,' Joudeh claimed.
Jordanian officials said they took special offence to posts on social media networks by Suleiman warning that advanced Soviet-designed Alexander missiles could target the kingdom when the US military deploys at least two Patriot missile batteries later this month.
Officials fear Assad's wrath after he threatened Jordan last April that it would be "playing with fire" if it supported foreign-backed terrorist groups.
Washington said earlier that it would be making Patriot batteries and advanced F-16 fighter jets available for annual war games scheduled later this month in the kingdom.
The United States announced in April it was dispatching over 200 army planners to Jordan.
Suleiman drew parallels between Jordan's deployment of Patriots and their deployment in Turkey earlier this year.
"The arrival of the Patriots in Turkey and stationing them on the border was a bad omen for the government of (Turkish Prime Minister) Tayyip Erdogan and we don't wish the same fate for those counting on the Patriots, " Suleiman said, referring to anti-government protests in Turkey.