I went back and watched the ABs because of SF's typical hyperventilating, and because at the time I thought it was a good idea to stretch Zimmermann out as his season is winding down.
Generally when you are looking for pitcher fatigue you look for pitches elevating above the zone. Zimmermann had two high fastballs in those two ABs, but he bounced back after both of them. The slider was the pitch that was really missing. He also ended both of those ABs with very solid pitches -- the ground out and the almost strike.
Anyway, I think that Zimmermann deserved to stay in the game. He was pitching a great game, it's late in the season, and we need him to be able to go deep into games in the future.
Davey's going to keep pushing his pitchers to go deeper into games, to get out of their own jams. It's a long run strategy. You can't yank him at the first sign of trouble, then pitch Clippard 3 innings, and repeat the next night.