Hundreds of protesters rushed the ceasefire line, cutting through barbed wire as they tried to enter the Golan Heights in a repeat of demonstrations last month that saw thousands mass along Israel's north.
Similar protests were held in the West Bank and in the Gaza Strip.
In Majdal Shams, on the occupied Golan, Israeli troops opened fire as demonstrators sought to push through the mined ceasefire line, which had been reinforced with several rows of barbed wire blocking access to a fence.
"Despite numerous warnings, both verbal and later warning shots in the air, dozens of Syrians continue to approach the border and IDF (Israel Defence Forces) forces were left with no choice but to open fire towards the feet of protesters in efforts to deter further actions," an army spokesman told AFP.
The United States called for calm.
"We are deeply troubled by events that took place earlier today in the Golan Heights resulting in injuries and the loss of life," the State Department said in a statement.
"We call for all sides to exercise restraint. Provocative actions like this should be avoided."
The US statement emphasised that "Israel, like any sovereign nation, has a right to defend itself."
The Israeli military also said that one person was wounded when at least one landmine exploded on Syria's side of the border.
"A Syrian mine exploded, seemingly because Molotov cocktails thrown at (Israeli) forces started a bush fire which caused the explosion of the mine, a number of mines even," an army spokeswoman told AFP. "Apparently there is one person wounded on the Syrian side."
Israeli public radio said "many" people were hurt in the explosion near Quneitra, which lies in no-man's land. There was no immediate confirmation from Syria.
In Majdal Shams, locals pleaded with soldiers to stop firing as troops used loudspeakers to warn demonstrators in Arabic that "anyone who comes close to the fence will be responsible for their own blood."
Israeli forces were on high alert after activists in the West Bank and Gaza, and in Arab nations bordering the Jewish state, called for protesters to march on Israeli checkpoints and border areas.
Military spokeswoman Lieutenant Colonel Avital Leibovitz accused Syria of orchestrating the Golan protest to deflect attention from deadly domestic anti-regime demonstrations.
"We believe that the Syrian regime is focusing the world's attention on the border with Israel instead of what is happening there," she said.
Israeli Prime Minister Benjamin Netanyahu called the Golan demonstrators "extremist elements" who "are trying to break through our borders and threaten our communities and our citizens."
Protests were also staged in Gaza and the West Bank, where 16 demonstrators were taken to hospital with light wounds from rubber bullets, and another 20 were treated for tear gas inhalation.
Around 100 people demonstrated in central Hebron in the southern West Bank, while dozens of protesters tried to march from the northern West Bank village of Deir al-Hatab to the nearby Elon Moreh settlement.
|Demonstrators prepare to evacuate a wounded fellow protestor who was hit by Israeli fire while trying to cut through a line of barbed wire and head into the Israeli-annexed Golan Heights|
In Gaza, Hamas police arrested around a dozen protesters who broke away from a rally at the northern town of Beit Hanun, and tried to march to the Erez border crossing with Israel.
Sunday's protests, timed to coincide with the 44th anniversary of the Six-Day War when Israel captured the Golan from Syria as well as the West Bank and Gaza Strip, were planned as a repeat of massive demonstrations last month.
On May 15, thousands of protesters massed on Israel's borders with Syria, Lebanon and Gaza, trying to force their way across on the anniversary of Israel's creation.
Israeli fire left six demonstrators dead on the Lebanese side of the border and four dead on Syria's side.
In Lebanon, Palestinian refugees on Sunday staged a day of mourning but the Lebanese army banned any gatherings at the border to avoid a repeat of the violence.