Some 170 people were allowed to pass overnight and additional small groups were accepted during the day, an AFP reporter said.
It was the first group of Syrians and Iraqis permitted to continue their desperate journey to Europe since dawn on Monday, when another 300 were let through before the frontier was closed.
With anger mounting, hundreds had tried to break through the border fence but were blocked by Macedonian police who fired tear gas at them, prompting a disapproving response from the EU.
Since then, Skopje has deployed additional police and troops to the border as a ‘protective’ measure, officials said.
At the Greek border crossing of Idomeni, local officials said there were 7,000 people in two camps operated by aid groups, with another 3,000 camping in the surrounding fields.
Over the past few days, aid groups have reported a shortage of food and tents, warning that the wet weather was taking a toll on the refugees, many of whom have children.
Macedonia also reported that its reception centre at the border with Serbia was nearing capacity with nearly 1,000 people there waiting to cross.
More than half of them are Afghans who are no longer allowed to go further into Europe.
‘Some 597 are from Afghanistan and are still waiting for a solution to be found as they have been here 12 days,’ said Goran Stojanovski, coordinator of the Tabanovce centre.
‘The others are mainly from Syria and Iraq returned from Serbia, and since Monday about 180 migrants from Syria and Iraq who have remained on no-man's land between Serbia and Macedonia for two days after not being allowed to enter Serbia,’ he told reporters.
- EU emergency aid plan -
The European Union on Wednesday unveiled a 700-million-euro emergency aid plan, over three years, for Greece and other states hit by the migrant crisis.
Greece has asked for around 480 million euros ($520 million) to help shelter 100,000 migrants as Europe faces its biggest wave of refugees since World War II in a crisis that has sown deep discord and threatened the bloc's solidarity.
On Tuesday, Athens boycotted a meeting of regional police chiefs in Belgrade to protest border-tightening decisions taken in its absence at a similar meeting in Zagreb in February, the Greek police ministry said.
At the time, the Balkan states and Austria agreed to restrict the passage to migrants while Greece sought to keep borders open until a migration summit can be held with Turkey next Monday.
Acting Serbian police chief Vladimir Rebic told N1 television that the Tuesday meeting in Belgrade ‘agreed it was necessary to maintain the additional border checks...to prevent illegal migration.’