DENVER — Yes, it was embarrassing, the way the reigning AFC champions did whatever they wanted to the 49ers. It certainly was discouraging the way key players failed to show up.

But let’s be real: The only thing this loss really hurts is the 49ers’ pride. The 42-17 defeat to the Broncos on Sunday night displayed only what close followers already knew: The 49ers are not where they need to be.

All Denver quarterback Peyton Manning did, in addition to throwing four scores to set the NFL record for touchdown passes, was obliterate any notion that the 49ers are one of the league’s elite teams. But that was a false premise anyway with all the 49ers are missing from the lineup.

“The best thing we can do is clear our heads of this,” said All-Pro linebacker Patrick Willis, who was forced to watch from the sidelines. “Watch film and see what we could’ve done better, clear our heads going into this bye week and come back ready for the second half.”

Truth is the 49ers could have lost this game even at full strength. Certainly, nothing has changed as far as the outlook of the season.

The 49ers’ best hope still is to hang on until they are at full strength, win the winnable games and see if they can make some magic happen late in the season.

That realistically has been the case since NaVorro Bowman blew out his knee in the NFC Championship game in January. Since Aldon Smith was arrested in the Los Angeles airport and eventually suspended for nine games. Since training camp, when the offensive line became a mystery mix because of injuries and Alex Boone’s holdout.

The comeback wins preceding Sunday’s blowout weren’t a sign the 49ers had arrived. It was a blueprint for how they survive this season. Scrap out every win they can against teams they can manhandle. But when it comes to the top-tier teams, the 49ers are going to struggle as long as backups are plugging holes in the lineups.

Losing to the Broncos on the road is no season-killer. The blowout nature of the loss was largely a result of the 49ers’ wealth of injuries and the short week after playing Monday night.

And the greatness of Manning.

“You’re playing against a coordinator when he’s out there,” safety Eric Reid said. “They get to the line quickly so they can see the defense. He can make a read. He can make a check. I think he calls whatever he wants to by what he sees, and it’s working for them.”

The only real concern coming out the debacle in Denver is whether the 49ers will ever get healthy enough to be serious contenders.

Bowman’s return isn’t a lock, and there is no telling how good he will be if he does return. Who knows how long it will take for Smith to round into form after his suspension ends.

Now, they might have lost their starting center for the rest of the season as Daniel Kilgore was carted off after apparently breaking his left leg. Left guard Mike Iupati missed the game with a concussion. Right tackle Anthony Davis returned from injury and isn’t anywhere near the dominant lineman he can be.

It’s hardly surprising the running game never got going, and the pass protection was a mess. Colin Kaepernick was sacked six times, and that doesn’t count the times he pressed the B button to escape from a swarm of Broncos.

There is nothing shocking about Peyton Manning torching a 49ers defense down six regulars.

The 49ers went up against the third highest-scoring offense in the league (29.4 points per game) without Willis, starting cornerback Chris Culliver and nickel back Jimmie Ward. That’s in addition to not having stud linebacker Bowman, sack specialist Smith and starting nose tackle Glenn Dorsey.

And Tramaine Brock, who hasn’t played since turf toe knocked him out in the season opener, looked as though he returned a week early. Most of Broncos receiver Demaryius Thomas’ 171 yards came with Brock well behind him — including the record-setting touchdown reception that put Manning ahead of Brett Favre on the all-time list.

“He’s awesome. He’s a Hall of Famer for sure,” 49ers linebacker Ahmad Brooks said of Manning. “On the flip side, on our end, it’s just one game. We have a bye week. We get a chance to bounce back and regroup … It’s a lot of key guys out. That’s all I can say.”

The 49ers get a week to rest up. Then they face four teams currently with losing records before the Thanksgiving Day showdown against the Seahawks, who lost their second straight game Sunday.

Winning those four games, and heading into the big rivalry game at 8-3, would certainly lessen the humiliation they endured at the hands of Manning on Sunday night.

It’s not a guarantee that when they get all their players back, and in a rhythm together, the 49ers will be elite. But that’s not a real possibility until their horses get back on the field.

If they are that team, that’s when we’ll find out. Not from this Sunday night spanking.

“We’ll be fine,” running back Frank Gore said after totaling 20 yards on nine carries. “When everybody gets back, we’ll be fine.”

Read Marcus Thompson II’s blog at blogs.mercurynews.com/thompson. Contact him at mthomps2@bayareanewsgroup.com. Follow him on Twitter at twitter.com/ThompsonScribe.