Gunfire from Syria raked a crowd at Al-Boqayah crossing near the town of Wadi Khaled, killing the Syrian woman and wounding five people including a Lebanese soldier, a Lebanese security official and an AFP correspondent said.
The shooting came as hundreds of Syrians fled violence in their homeland on foot into Lebanon.
At one point, an armed man in plainclothes waded towards Al-Boqayah across the river which marks the border but was turned back by Lebanese civilians and fled firing shots into the air.
The area around Al-Boqayah was later deserted apart from Lebanese soldiers, a Red Cross team and several reporters, an AFP correspondent at the scene said.
The latest incidents came as Pope Benedict XVI called for an end to the bloodshed in Syria and urged authorities and citizens to strive for a "future of peace and stability."
"I ask God that there be no further bloodshed in (Syria), this country of great religions and civilisations," the pope said after his weekly Angelus prayer in Rome's St Peter's Square.
Since Saturday, residents of the western Syrian town of Tall Kalakh, which is encircled by the Syrian army, have fled in their hundreds into nearby northern Lebanon.
According to a witness and a hospital worker in Tall Kalakh, security forces shot dead at least four people and wounded several others Saturday as thousands held a second day of anti-regime protests.
A witness in Tall Kalakh told AFP that residents had been treating the wounded in a small clinic rather than the town hospital to prevent the casualties from being arrested or "finished off."
Security forces on Saturday fired at a funeral convoy at an entrance to the town, killing the mother and wounding three family members of a victim of the clashes, according to the Tall Kalakh resident.
Al-Watan newspaper, which is close to the regime, said on Sunday that armed men had fled the cities of Banias and Homs and sought refuge in Tall Kalakh, while "fighters" from Lebanon had entered Syria.
Tall Kalakh was the scene of "heavy fighting" on Saturday night between the Syrian army and armed groups, the daily said.
The mayor of the Lebanese town of Moqaibleh, Rami Khazaal, estimated that almost 1,000 refugees had fled across the border into northern Lebanon on Saturday.
At least five were hospitalised with gunshot wounds, one of whom died, said a source at Qobbayyateh hospital said.
The latest bloodshed cast a pall over the government's pledges to forge ahead with reforms in Syria, where the first pro-reform protests broke out on March 15, and have triggered fresh condemnation from Western governments.
At least five people were killed in protests on Friday in the central city of Homs and a Damascus suburb, activists said, despite an order from Assad for security forces not to open fire.
Information Minister Adnan Mahmud announced later the same day that a "national dialogue" would be launched as soldiers withdrew from flashpoint cities and towns such as Banias on the Mediterranean coast and Daraa in southern Syria.
An activist in Banias, meanwhile, said tanks had been withdrawn from the town centre but security forces were still deployed on Sunday.
Up to 850 people have been killed and at least 8,000 arrested since the protests started in mid-March, human rights groups say. The regime has blamed the deadly violence on "armed terrorist gangs" and kept out the foreign media.
An editorial headlined "Game Over" in the government newspaper Tishrin commented on Sunday that it was clear the revolt was losing steam.
"The game is over and those betting on destroying Syria from within have failed without finding a way to sow discord," it said, dismissing the protesters as "suicidal" and "unconscious".