In this work, an advanced 2D nonparametric correlogram method is presented to cope with output-only measurements of linear (slow) time-varying systems. The proposed method is a novel generalization of the kernel function-based regularization techniques that have been developed for estimating linear time-invariant impulse response functions. In the proposed system identification technique, an estimation method is provided that can estimate the time-varying auto- and cross-correlation function and indirectly, the time-varying auto- and cross-correlation power spectrum estimates based on real-life measurements without measuring the perturbation signals. The (slow) time-varying behavior means that the dynamic of the system changes as a function of time. In this work, a tailored regularization cost function is considered to impose assumptions such as smoothness and stability on the 2D auto- and cross-correlation function resulting in robust and uniquely determined estimates. The proposed method is validated on two examples: a simulation to check the numerical correctness of the method, and a flutter test measurement of a scaled airplane model to illustrate the power of the method on a real-life challenging problem.