The about-face came as EU foreign policy chief Federica Mogherini began her first visit to the region since a new rightwing Israeli government was sworn in last week.
The three-month pilot project barring Palestinian workers from returning home from Israel to the West Bank on Israeli buses began on Wednesday morning after approval from hardline Defence Minister Moshe Yaalon.
It was immediately attacked by rights groups and the opposition, who denounced it as an "unprecedented" move that heaped unnecessary humiliation on the Palestinians and would ultimately damage Israel.
"I have nothing but regret for the discordant voices that we heard this morning, supporting the separation between Jews and Arabs on the basis of ideas that have no place being heard or said," he said in a statement.
Palestinian president Mahmud Abbas told Mogherini when they met in the West Bank town of Ramallah that the new Netanyahu government posed a threat to resolving the Palestinian-Israeli conflict.
"All of our efforts now are to save the two-state solution from an Israeli government that chose settlements," Palestinian negotiator Saeb Erakat quoted him as saying.
"I support the vision of two states for two peoples; a demilitarised Palestinian state that recognises the Jewish state," he said.
"I believe your recommitment tonight to work on peace and security," Mogherini responded.
In annexed east Jerusalem earlier on Wednesday, a Palestinian driver rammed his car into two border policewomen, moderately injuring them, before he was shot dead by another officer, police said.
Tens of thousands of Palestinians travel each day to work in Israel, mainly in construction.
But it was quickly stopped by Netanyahu, an official in his bureau told AFP.
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