From what I read, he didn't complain about it. When asked about the Bengals throwing late in the 4th quarter with a 20-point lead, Harbaugh said, "They call their plays, we call ours."
You could see read his lips when he met Taylor for the handshake after the game asking why they called that pass. He was pissed and you could tell it. Watch the video.
He knew better than saying something publicly but he sure as hell said something to Zac Taylor.