This paper presents the time synchronization infrastructure for a low-cost run-time platform and application framework specifically targeting Smart Grid applications. Such distributed applications require the execution of reliable and accurate time-coordinated actions and observations both within islands of deployments and across geographically distant nodes. The time synchronization infrastructure is built on well-established technologies: GPS, NTP, PTP, PPS and Linux with real-time extensions, running on low-cost BeagleBone Black hardware nodes. We describe the architecture, implementation, instrumentation approach, performance results and present an example from the application domain. Also, we discuss an important finding on the effect of the Linux \texttt{RT\_PREEMPT} real-time patch on the accuracy of the PPS subsystem and its use for GPS-based time reference