"Fire emanating from Syria into Israel will not be tolerated and shall be responded to with severity," the Israeli army said in a statement.
Haaretz reported the retaliatory warning shot was the first time since the Yom Kippur War in 1973 that Israel had fired on Syria.
Ynetnews.com reported the Israeli artillery corps fired a Tammuz missile in the direction of a post in Syria after the 120mm mortar shell struck in Israel.
The mortar shell caused no damage or injuries, while an Israeli military spokesman said it wasn't known if the Israeli shot likewise caused no harm.
The mortar shell fired from Syria apparently was not intentionally fired at Israel, but appeared to have been fired during clashes between Syrian regime and rebel forces in villages not far from the Israeli border, Israel Radio reported.
The incident occurred just days after three mortar shells fired from Syria landed in Israel's central Golan Heights. Two of the shells exploded in open fields and one landed in the community of Moshav Alonei HaBashan, but failed to explode.
Earlier last week, Israel submitted a complaint to the United Nations charging Syria with violating the Israeli-Syrian cease-fire agreement after three Syrian tanks entered the demilitarized zone near the Israeli border. In a separate incident, an Israeli army jeep patrolling near the border came under fire.
Brig. Gen. Yoav Mordechai, an Israeli military spokesman, said there have been a total of eight such events in the past two months.
While touring Israel's northern border last week, Lt. Gen. Benny Gantz, the Israeli chief of general staff, warned the situation in Syria could become Israel's affair. "This is a Syrian issue that could become our issue," he said.
Israel has tried to stay out of the civil war raging in Syria.
"For the first time since the Yom Kippur War, fire was aimed at a Syrian post," Mordechai said. "We don't know whether there are any casualties on the Syrian side.
"We also notified the U.N. of the incident and repeated the warning given to Syria, that the IDF [Israel Defense Forces] will not tolerate any fire on Israel. We will be monitoring the situation to see if the message was received."