While the United States has made clear it wants better ties with Syria, which appears on the US list of state sponsors of terrorism, the renewal of the sanctions shows it is not yet ready for a dramatic improvement.
US officials said on Friday that Obama had signed the executive order the previous day.
"We continue to have serious concerns about Syria's actions," said Robert Wood, the US state department spokesman.
"We need to see concrete steps from the Syrian government to move in another direction."
The decision coincided with renewed high-level diplomatic contacts with Damascus this week.
Jeffrey Feltman, a senior state department official, and Daniel Shapiro, a White House National security council official, met Walid al-Moualem, the Syrian foreign minister on Thursday.
"I would like to emphasise that there will be no deals made at Lebanon's expense with Syrians or others"
US deputy assistant secretary of state
The two US envoys told Syrian officials that the United States was committed to pursuing a peace deal between Syria and Israel, a main foreign policy objective for Damascus.
"We conveyed ... president Obama's sincere commitment to pursue Arab-Israeli peace on all tracks, including on the Syrian-Israeli track," Feltman said after the meeting.
Syria held indirect Turkish-mediated talks with Israel last year, but the discussions were called off during Israel's 22-day offensive on the Gaza Strip, which ended in January.
Damascus is believed to want the US involved in any future negotiations.
The meeting also discussed Syria's role in Iraq and Lebanon as well as its relationships with armed groups across the Middle East, according to sources familiar with the meeting.
However, another senior US envoy said on Friday in the Lebanese capital, Beirut, that progress with Syria would not come at Lebanon's expense.
"As we expand our regional engagement here in the Middle East, I would like to emphasise that there will be no deals made at Lebanon's expense with Syrians or others," David Hale, US deputy assistant secretary of state, said.
The US withdrew its ambassador to Damascus in 2005 to protest against Syrian involvement in Lebanon.
Washington has criticised Syria for supporting groups such as the Palestinian Hamas movement in Gaza and Lebanon's Hezbollah.
It has also accused Syria of not doing enough to stop fighters crossing into Iraq to launch attacks on foreign forces.
"We've said to you before our concerns about what Syria is doing in Iraq, its support for terrorist groups. We've encouraged the Syrians to play a positive role in the Middle East," Wood said.