Merkel's two-day visit came four months after Greece emerged from its third and final bailout package.
Macedonia's government has vowed to push ahead with changing the country's name to appease Greece and build ties with the West, but opponents said low turnout made it illegitimate.
Macedonia's citizens will vote Sunday on whether to rename their country "The Republic of North Macedonia", part of a compromise with Greece which has a province with the same name.
Kurz has advocated for stronger border security as the European Union grapples with the continued arrival of migrants and the management of its internal and external borders.
After years of stinging austerity measures, Greece emerges from its third and last bailout, although officials warn the country still has a "long way to go".
Greece has received the final 15-billion-euro payment from its eight-year bailout programme in what creditors hailed as proof that tough austerity measures were "paying off".