The Yankees spent most of the weekend suffocating the Padres’ offense.

Then Schmidt happened in the sixth inning Sunday, though Clarke Schmidt wasn’t exactly to blame.

Against Schmidt and two relievers, the Padres finally broke out for a four-run rally on an error, a fielder’s choice, two walks and three singles (one bunt and one swinging bunt) to avoid a sweep and hand the Yankees a 5-2 loss at Petco Park.

Schmidt had taken a shutout into the sixth inning, with the Yankees (37-18) giving him a 1-0 lead in the top of the frame on Juan Soto’s RBI double.

Manny Machado celebrates after a hit for the Padres in their win against the Yankees on Sunday

But the wheels fell off from there as the Padres (28-28) snapped the Yankees’ four-game winning streak heading into an off day on Memorial Day.

Schmidt allowed the first two batters to reach in the bottom of the sixth — Jake Cronenworth on a ground ball that went right under the backhanded glove of Gleyber Torres for his seventh error of the season and Manny Machado on a five-pitch walk.

That marked the end of Schmidt’s day, though he still became the 14th straight Yankees starter to throw at least five innings and allow two runs or fewer — tying the MLB record since 1893.

Anthony Rizzo bobbles a bunt during the Yankees’ win against the Padres on Sunday

But the Yankees bullpen did not provide much relief. Lefty Victor Gonzalez entered and walked pinch-hitter Donovan Solano on five pitches to load the bases.

Jackson Merrill then hit a one-hopper to Anthony Rizzo that he snared and threw to second for the force out, but Cronenworth scored from third to tie the game.

Clarke Schmidt pitched into the sixth inning for the Yankees on Sunday

Ha-Seong Kim came up next and laid down a well-placed bunt between the mound and first base.

Rizzo tried to barehand it to have a play at the plate, but he could not pick it cleanly and the Padres took a 2-1 lead.

Then with two outs, Luis Arraez lined a single back up the middle off Gonzalez for the 3-1 lead before Fernando Tatis Jr. got off a check-swing dribbler down the third-base line off Dennis Santana to make it 4-1.

Juan Soto drove in the Yankees’ first run Sunday against the Padres

Ha-Seong Kim came up next and laid down a well-placed bunt between the mound and first base.

Rizzo tried to barehand it to have a play at the plate, but he could not pick it cleanly and the Padres took a 2-1 lead.

Then with two outs, Luis Arraez lined a single back up the middle off Gonzalez for the 3-1 lead before Fernando Tatis Jr. got off a check-swing dribbler down the third-base line off Dennis Santana to make it 4-1.

Alex Verdugo hit a solo home run to lead off the ninth inning, but that was as close as the Yankees would get.

Schmidt and Joe Musgrove spent the first five innings trading zeroes while working around traffic before the Yankees finally scored first in the top of the sixth.

Anthony Volpe extended his hitting streak to 19 games Sunday

Anthony Volpe extended his career-high hitting streak to 19 games with a single lined up the middle and then stole second base, his 11th swipe of the year.

That set him up to score when Soto roped a line drive past the reach of Tatis to put the Yankees up 1-0.

With Schmidt being charged for a pair of runs in the bottom of the inning — only one of them earned — the Yankees starters’ scoreless streak came to an end at 30 ¹/₃ innings.

The Padres later padded their lead in the seventh when Cronenworth and Machado hit back-to-back doubles off Caleb Ferguson.