By Morris Phillips

The third pre-season game is supposed to provide the truest glimpse of how an NFL team might perform in their season opener, so instead of exhaling in celebration of their first exhibition win of the season, the 49ers answered a bunch of questions about their substandard pass protection in a 21-7 win over the Chargers.

With the first team offense in the game, Colin Kaepernick was a very pedestrian 6 of 12 for 59 yards while being sacked once.  In three appearances, the 49ers have yet to score a touchdown with the presumptive starter behind center and in this one, the absence of tackle Adam Boone and the poor play of All-Pro guard Mike Iupati were obvious reasons for the lack of success.

It wasn’t until backup Blaine Gabbert opened the second quarter and found Vance McDonald for the first touchdown of his NFL career, and the first touchdown by the 49ers in Levi’s Stadium that things started to look up.  But, as coach Jim Harbaugh admitted afterwards, there remains a bunch of work to do in the San Francisco trenches.

“Well, I know we got edged on the one,” Harbaugh said.  “Then the second (breakdown), they got us on a twist where we got hit and fumbled.  Go to work on that.  Got to be good in thatea.”

“Execution,” Kaepernick answered when asked about the first-team offense.  “We have good plays, we just didn’t execute.”

The 49ers figure to be much improved on offense even if the difference from last year is that Kaepernick is a year wiser and stronger.  But the offensive line provides a real concern with one starter not in camp and others—like Iupati—struggling in Boone’s absence.

Defensively, the 49ers were dandy, bending a bit while defending quarterback Philip Rivers in what will likely will the veteran Chargers’ quarterback’s final pre-season look as well.  Rivers was 9 of 10 passing, and his backup Brad Sorenson was 11 for 21, but the Chargers were held to just one score—with Rivers at the helm—and then shut out in the second half.

The 49ers conclude the exhibition season Thursday in Houston with the Texans.