Formation of ordered magnetic states in germanium nanostructures embedded in SiO2 has been investigated. Samples with the nanostructures were prepared by sputtering deposition on Si(100) substrates, followed by thermal annealing in vacuum. Transmission electron microscopy, energy dispersive X-ray spectrometry, and Raman spectroscopy have been used to characterize the samples. Magnetic measurements were performed using a superconducting quantum interference device. Size-effect induced magnetic orderings in the germanium nanostructures were found to be present at room temperatures and below. Superparamagnetic behavior was observed at temperatures above 230 K, whereas thermal excitation of spin reorientation and magnetic coupling has been revealed at temperatures below 60 K. Inverted hysteresis loops with negative remanences and multiple plateaus revealed the ferri- or antiferromagnetic nature of the coupling. Inter-domain coupling and effect of magnetic anisotropy will be discussed based on the experimental results and simulations with a spin reorientation model.