SAN DIEGO -- The first inning has become a real problem for Brian Johnson, and it cost him and the Red Sox for a second straight start.

Filling in for the injured Chris Sale on Sunday at Petco Park, Johnson again gave up three runs in the first inning. And again, Boston didn’t recover, suffering a 3-1 loss that prevented what could have been a three-game sweep against the Padres.

• Box score

In the seven starts he has made this season, Johnson has an ERA of 11.57 and an opponents’ batting average of .394 in the first inning.

Look for Johnson to huddle with the coaching staff and make some adjustments prior to his next start, which could be next week in Anaheim unless David Price is back by then.

“I’m just not as sharp in the first as I am in other innings,” Johnson said. “Maybe you’ve got to change things up for me a little bit, maybe switch the game plan. Seems to be working when I go in the second or third inning [as opposed to the first], so maybe it’s a game-plan thing.”

This time, the big blow was a two-run homer by Manny Machado on a misfired curveball.

“I feel like, for me, the first inning has been sloppy,” said Johnson. “I hung a curveball to Machado. Curveball down to [Manuel] Margot was a good pitch, I thought, and he put a good swing on it. I didn’t elevate high enough to [Francisco] Mejia, kind of sloppy first inning for me. Biggest one was hanging a curve to Machado.”

The two starts since Johnson replaced Sale (out for the season) in the rotation have been nearly identical. In both games, Johnson settled in after the tough start, the bullpen dominated and the Red Sox didn’t give up another run. But magnifying Johnson’s struggles is that the high-powered offense went nearly silent in both games, losing 3-2 to the Phillies before Sunday’s tight loss.

At this point, Cora doesn’t appear to be contemplating a change in the rotation. He also doesn’t have many other options.

“Like I said last week, the opposition scores three in that spot [in the rotation], we’ll take it. Just have to hit in that spot,” said Cora.

Thanks to some stout Boston defense, the lead didn’t get any bigger.

In the bottom of the third, Ty France roped a double into left and Eric Hosmer tried to score from first. But J.D. Martinez got the relay in quickly to shortstop Xander Bogaerts, who fired home to nail Hosmer.

“That was a huge play,” said Red Sox center fielder Jackie Bradley Jr. “Perfect replay by J.D. and by Bogey as well. Good tag by Christian [Vazquez]. All around, it was a pretty great play. Bang-bang and everything needed to be perfect to make that play.”

And after Martinez inched the Sox a little closer with a solo shot in the fourth, Jackie Bradley Jr. started the bottom of the inning by making a tremendous leaping grab on a drive to deep center by Luis Urias. Bradley jumped up, hung on the wall and extended his glove to make the catch.

"Just get back there and time up my leap," Bradley said. "I didn’t have to necessarily get on the wall. It’s one of those ones where the wind is blowing out a little bit, so I’d rather get up there and ask questions later.”

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From then on, the Red Sox waited for the big hit, but it never came.

The golden opportunity was the top of the eighth, when Boston had runners on first and second with nobody out after Machado booted Mookie Betts' routine grounder to third base. But Padres flame-throwing reliever Andres Munoz got Rafael Devers on a 4-6-3 double play and struck out Martinez on a slider. Three times in the seven-pitch at-bat, Munoz pumped in fastballs at 101 mph or faster.

“I mean, 102 from their guy,” said Cora. “Ground-ball double play and good pitches to J.D. The 1-2 slider is pretty tough. You see the numbers from Munoz, he’s pretty good.”

At another juncture of the season, the Red Sox might have been able to wash this one away more easily, chalking it up to coming up on the short end of a good baseball game.

But with 30 games left in their season, the Sox trail the Rays by six games in the American League Wild Card standings and Oakland by 5 1/2. Both teams lost on Sunday, meaning a sweep in San Diego would have allowed the Sox to chip a full game off the deficit against all the teams they are chasing. This marked the third time in the last month Boston had a chance to sweep a series, only to lose the final game.

“It’s always important [to close out a sweep],” said Cora. “We’re running out of time. But we’ll take two out of three. We played good baseball today, but we didn’t hit.”

Though the odds might seem long for the defending World Series champs to get back to October, Cora isn’t ready for any type of concession speech.

“We’re good,” Cora said. “We’re not where we want to be. We’ll talk about it Sept. 1. We get there and see where we’re at and go from there.”

If the Red Sox are going to do the improbable and advance to the postseason, they are going to need to get on the type of run they haven’t had since last season.

“Got a long ways to go,” said Bradley. “I’m not saying the amount of games, but I’m saying for us as a whole. We feel like we’re not where we want to be. All we can do is control what we can control and continue to play hard, compete and win ballgames and see where we lie at the end.”