Hundreds of people had been stranded on the Egyptian side of the Rafah border terminal since June 25 when it was closed following the capture of an Israeli soldier by Palestinian gunmen.
A spokeswoman for the European Union border monitors said the terminal would be open for humanitarian cases for 11 hours on Tuesday but there was no guarantee the border will open again on Wednesday.
The Israeli defence ministry said a decision would be taken on Tuesday evening on whether to keep the border open indefinitely
The border terminal – the only crossing into the Gaza Strip which does not involve entering Israel - was opened following an agreement between EU observers, the Palestinian Authority and Israel.
"We've been stuck under the burning sun, without shade in the desert since they closed the terminal," said Qussai Abu Ahmad, returning from Egypt where his wife had gone for an operation.
"It was a tragic situation. There was no water, the people spent all their money, the suffering," he said as he crossed with his wife and two sons.
The road between Rafah and El-Arish, the biggest town in northern Sinai, was filled with cars and minibuses carrying Palestinians toward the border when it reopened.
Last Friday, Palestinian gunmen blew a hole in a wall on the border near the terminal, allowing about 1,000 people to cross before an Israeli helicopter fired warning shots, forcing a crowd to disperse.
The EU has observers at Rafah, at the request of the Palestinian Authority and Israel, to monitor agreements on border traffic.
The border reopened last November, two months after Israel withdrew from the Gaza Strip following a 38-year occupation, under an Israeli-Palestinian agreement brokered by the United States.