Six Day War Battle in Golan Heights: False Egyptian reports of a crushing victory against the Israeli army and forecasts that Egyptian artillery would soon be in Tel-Aviv influenced Syria's willingness to enter the war. Syrian leadership, however, adopted a more cautious approach, and instead began shelling and conducting air raids on northern Israel. When the Israeli Air Force had completed its mission in Egypt, and turned around to destroy the surprised Syrian Air Force, Syria understood that the news it had heard from Egypt of the near-total destruction of the Israeli military could not have been true. During the evening of June 5, Israeli air strikes destroyed two-thirds of the Syrian Air Force, and forced the remaining third to retreat to distant bases, without playing any further role in the ensuing warfare. A minor Syrian force tried to capture the water plant at Tel Dan (the subject of a fierce escalation two years earlier), Kibbutz Dan, and She'ar Yashuv. But a broader Syrian offensive quickly failed. Several Syrian tanks are reported to have sunk in the Jordan River. Other problems included tanks too wide for bridges, lack of radio communications between tanks and infantry, and units ignoring orders to advance. A post-war Syrian army report concluded "Our forces did not go on the offensive either because they did not arrive or were not wholly prepared or because they could not find shelter from the enemy's planes. The reserves could not withstand the air attacks; they dispersed after their morale plummeted." The Syrian command abandoned hopes of a ground attack and began a massive shelling of Israeli towns in the Hula Valley instead.

On June 7 and June 8, the Israeli leadership debated about whether the Golan Heights should be attacked as well; the attack on Syria was initially planned for June 8, but was postponed for 24 hours. At 3 AM on June 9, Syria announced its acceptance of the cease-fire. Despite this, four hours later at 7 AM, Israel’s minister of defense, Moshe Dayan, “gave the order to go into action against Syria.” In addition to long-standing Israeli claims on the Mt Hermon area, Syria also had supported the pre-war raids that had helped raise tensions and had routinely shelled Israel from the Heights, so some Israeli leaders wanted to see Syria punished. Military advice was that the attack would be extremely costly, since assailing the heights would be an uphill battle against a strongly fortified enemy. The western side of the Golan Heights consists of a rock escarpment that rises 500 metres (1700 ft) from the Sea of Galilee and the Jordan River, and then flattens to a more gently sloping plateau. Moshe Dayan believed such an operation would yield losses of 30,000 and opposed it bitterly. Levi Eshkol, on the other hand, was more open to the possibility of an operation in the Golan Heights, as was the head of the Northern Command, David Elazar, whose unbridled enthusiasm for and confidence in the operation may have eroded Dayan's reluctance. Eventually, as the situation on the Southern and Central fronts cleared up, intelligence estimated that the likelihood of Soviet intervention had reduced, reconnaissance showed some Syrian defenses in the Golan region collapsing, and an intercepted cable showed Nasser urging the President of Syria to immediately accept a cease-fire, Moshe Dayan became more enthusiastic about the idea, and he authorized the operation.

The Syrian army consisted of about 75,000 men grouped in nine brigades, supported by an adequate amount of artillery and armor. Israeli forces used in combat consisted of two brigades (one armored led by Albert Mandler and the Golani Brigade) in the northern part of the front at Givat HaEm, and another two (infantry and one of Peled's brigades summoned from Jenin) in the center. The Golan Heights' unique terrain (mountainous slopes crossed by parallel streams every several kilometres running east to west), and the general lack of roads in the area channeled both forces along east-west axes of movement and restricted the ability of units to support those on either flank. Thus the Syrians could move north-south on the plateau itself, and the Israelis could move north-south at the base of the Golan escarpment. An advantage Israel possessed was the excellent intelligence collected by Mossad operative Eli Cohen (who was captured and executed in Syria in 1965) regarding the Syrian battle positions. Syria had built extensive defensive fortifications in depths up to 15 kilometers, comparable to the Maginot Line.

As opposed to all the other campaigns, IAF was only partially effective in the Golan because the fixed fortifications were so effective. However, the Syrian forces proved unable to put up an effective defense largely because the officers were poor military leaders and treated their soldiers poorly; often officers would retreat to escape danger, leaving their men confused and ineffective. By the evening of 9 June, the four Israeli brigades had broken through to the plateau, where they could be reinforced and replaced. However, a battalion of the 8th armored brigade was ambushed after taking a wrong turn. 24 out of its 26 tanks were lost, and casualties amounted to 13 killed and 33 wounded.

On the next day, June 10, the central and northern groups joined in a pincer movement on the plateau, but that fell mainly on empty territory as the Syrian forces fled. Several units joined by Elad Peled climbed to the Golan from the south, only to find the positions mostly empty as well. During the day, the Israeli units stopped after obtaining manoeuvre room between their positions and a line of volcanic hills to the west. In some locations, Israeli troops advanced after an agreed-upon cease-fire to occupy strategically strong positions. To the east, the ground terrain is an open gently sloping plain. This position later became the cease-fire line known as the "Purple Line".

Time magazine reported: "In an effort to pressure the United Nations into enforcing a ceasefire, Damascus Radio undercut its own army by broadcasting the fall of the city of Quneitra three hours before it actually capitulated. That premature report of the surrender of their headquarters destroyed the morale of the Syrian troops left in the Golan area."