By dpa correspondents
A travel warning was already in place for Gaza, while travel to Israel and the Palestinian territories was previously "strongly discouraged."
The warnings come ahead of a widely expected offensive by Israel into Gaza, after militant Hamas, which rules the strip, launched large-scale attacks on Israel last weekend.
Berlin also continues to fly citizens to safety amid fears that the conflict will further expand.
German military transport aircraft which flew out passengers from Israel landed in Germany on Sunday morning, the armed forces in Berlin said.
One A400M transporter landed in Wunstorf, in the north-western German state of Lower Saxony, at 4:35 am (0235 GMT), the Bundeswehr said on social media platform X, formerly Twitter.
Another transport aircraft carrying 29 passengers landed at 7 am, with 29 passengers on board. A third plane has landed in Tel Aviv.
According to parliamentary defence spokesman Wolfgang Hellmich, both aircraft, which were sent off from Germany on Saturday, also took relief material to Israel.
Airline Lufthansa has been flying Germans out of Israel on special flights this week, with more than 800 flown to Germany on Friday alone.
But the German carrier said on Saturday it was pausing those flights due to security issues and "unresolved questions of operational stability in Tel Aviv."
The German Foreign Office said it has supported some 2,800 Germans leaving Israel via land, air and sea so far.
Several countries have been scrambling to get their citizens out of Israel since Hamas fighters launched thousands of rockets toward Israel, breached border defences and rampaged across communities of southern Israel a week ago.
The surge in violence was unleashed by Islamist organization Hamas which launched thousands of rockets toward Israel while hundreds of its fighters breached border defences in an unprecedented attack last weekend that left more than 1,300 dead.
Hamas is classified as a terrorist organization by the US, EU and Israel.
Israel responded by launching retaliatory airstrikes on the coastal enclave, where at least 2,329 people have been killed and more than 9,000 people injured.
The security situation in the region is set to remain extremely tense as the Israeli military says it is preparing for an "integrated and coordinated attack from the air, sea and land" on the Hamas-ruled Gaza Strip.