Techniques for tracking, by a host system, virtual machine (VM) memory modified by a physical input/output (I/O) device that supports I/O virtualization are provided. In one embodiment, a hypervisor of the host system can receive a hardware interrupt from the physical I/O device, where the hardware interrupt indicates that a virtual function (VF) of the physical I/O device has completed a direct memory access (DMA) write to a guest memory space of a VM running on the host system. In response to the hardware interrupt, the hypervisor can invoke a function implemented by a physical function (PF) driver of the physical I/O device, where the function is configured to inspect the VF's state in order to identify memory portions modified by the DMA write. The hypervisor can then mark, in a hypervisor-level page table, one or more memory pages corresponding to the identified memory portions as dirty pages.