Both countries -- former enemies in the 1990s war following the breakup of Yugoslavia -- have been embroiled in tit-for-tat restrictions caused by the human exodus washing through the Balkans.
Croatia closed all but one of its border crossings with Serbia and blamed Belgrade for diverting an unrelenting flow of migrants towards its frontier.
In Brussels, the European Commission said it was "urgently seeking clarifications" from Croatia, prompting Prime Minister Zoran Milanovic to announce he planned to remove border restrictions with Serbia shortly.
As thousands of migrants and refugees continued to stream through Croatia towards northern Europe, non-EU Macedonia said trucks with Macedonian number plates were also being affected by the restrictions.
Also Read
More than a hundred were stacked up at the frontier between both countries.
Deputy Economy Minister Hristijan Delev warned that if by Tuesday the border had not "re-opened", Macedonia, Serbia and other countries that were part of a central European free trade grouping "will have to meet to find a solution."
And as cold and rainy weather settled in, migrants -- some of them wearing just shorts and plastic sandals -- were seeking medical help at Croatia's Opatovac transit centre near Serbia, local media reported.
The huge influx started when Hungary sealed its border with Serbia to prevent refugees from using the country as a thoroughfare to western Europe.
The closure prompted the migrants to divert their route through Croatia instead, which was quickly overwhelmed.
Zagreb now buses a large majority of the migrants straight to the border with Hungary, and Prime Minister Viktor Orban said Friday Budapest eventually planned to seal its border with Croatia too.