The offense was pretty stinky although Harris was doing alright against a pretty good run defense. Overall his stats were 11 for 53 and 1TD, averaging 4.8 yards per rush. For additional context, you can pull out Harris' shortest and longest runs (outliers) which brings his rushing average to 3.7 yards. Cobb went 2 for 23 and Rodgers had 3 scrambles for 28. That's 104 rushing yards but here is the real meat:
The Packers went 3-and-out to start the game on 3 passes. On the Packers only TD of significance (not in garbage time), McCarthy/Rodgers called 2 pass plays and 5 rushes. Score! On the next three possessions, Harris got the ball twice each drive and gained 2 yards, 3 yards, 3 yards, 3 yards, 3 yards, and 3 yards resulting in an INT, a FG, and a punt on those three drives. There was decent commitment to the run in those drive (6 rushes on 14 plays) but low production. Harris touched the ball for the last time after only 1.5 minutes into the 2nd half. One could surmise that Harris wasn't gaining enough yardage, but they always say that a defense wears down as the game progresses.
At this point, McCarthy then switched to Randall Cobb rushing him twice out of the shotgun for 23 yards. That was truly the last time that McCarthy/Rodgers called a rushing play, not even half way through the 3rd quarter! To put that in perspective, after Harris' touchdown in the 1st quarter, Green Bay rushed on 8 of 46 plays - a 17% ratio! That's a pathetic rush/pass balance.
The game was close when McCarthy shut down Harris, with the score still 21-24. When Cobb had his two rushes the score was 24-31, just a one touchdown game and well within reach. IMO - The game was still close but McCarthy panicked and went into shotgun pass mode way too early, allowing the defense to shut down Rodgers and the 49ers to run away with the game.