City had defender Jordan Stewart sent off for his second yellow card on 65 minutes, but they were already two down at the time, and Walsall never let them off the hook.
Jamie Paterson opened the scoring in the 33rd minute and notched his 13th of the season to complete the scoring three minutes from the end.
Craig Westcarr hit the second goal from a 53rd-minute penalty and headed the third after Paterson's free-kick had been blocked.
Pressley said: "It was a great game but the disappointing thing was that it was spoiled by the sending-off.
"I thought Jordan in no way meant to foul the player who just clipped the ball away at the last moment. There was very little in it.
"I felt in the first half we were very unfortunate to be 1-0 down and were in control for long periods, handling the pressure of the game well, but the decision making in the final third was the difference.
"Obviously the penalty kick and sending-off changed things, but even after that credit to my players for still wanting to win the game. The second goal was completely against the run of play, but I'm not taking anything away from Walsall who are a very good side.
"I saw many good things in our play, although the result doesn't suggest that."