Ohlendorf, making his fifth start of the season and third after a stint in the Padres' bullpen, struggled early against Miami.
The Marlins plated a run in the first after the righty gave up a walk to Emilio Bonifacio to lead off the inning. Carlos Lee then hit a two-out RBI single before Ohlendorf could get out of the frame.
After working around a one-out walk in the second, Ohlendorf wasn't as fortunate in the third. Marlins pitcher Nathan Eovaldi led off the inning with a single -- just the second hit of his career -- and Jose Reyes took advantage of a changeup that Ohlendorf left up in the zone, sending a two-run shot to right field to put the Padres in a 3-0 hole.
It was the first home run Ohlendorf allowed since June 25 against the Astros -- his last outing before he was relegated to the bullpen. The home run was Reyes' seventh of the season, and it extended his hit streak to 15 games.
"Other than the third inning, I thought my command was really good," Ohlendorf said. "I was happy with how I was throwing in the first inning, even though I gave up the run. Aside from the third inning, I thought I was throwing well."
That's all the Marlins got against Ohlendorf, who retired the final 10 batters he faced. He recorded his third straight quality start, going the six innings on just 73 pitches, but the three runs were as many as he gave up in his previous two outings combined.
"I feel good about how I'm throwing," Ohlendorf said. "I've pitched well in the past like this, it's just been a while. But I feel really good about how I'm pitching now and feel like I'm getting back to what I'm capable of doing."
While the third-inning home run proved decisive, the Padres squandered several opportunities against the Marlins, stranding seven men on base and going 1-for-9 with runners in scoring position.
The Padres left five on through the first four innings against Eovaldi, whom the Marlins acquired on Wednesday in the Hanley Ramirez trade.
San Diego was unable to make anything of a one-out walk in the first. In the second, Yonder Alonso hit a one-out double, but was stranded.
The Padres had runners on first and second to lead off the fourth after Eovaldi hit Carlos Quentin with a pitch and then walked Yasmani Grandal. The righty retired the next three batters, however, to preserve the Marlins' lead.
"After I got on base, I got a little tired out there and I guess not being used to the heat was part of it," Eovaldi said. "I felt I got a little tired after that and then I hit Quentin and walked the next batter. You've got to battle through it and compete."
San Diego was able to manufacture a run in the sixth. Chase Headley hit a leadoff single, and Eovaldi got Quentin to fly out to center field. Grandal followed with a single of his own to put two aboard for Alonso, who slapped a double, his second of the night, to right field to score Headley and cut the deficit to 3-1.
The Padres had a chance with the tying runs on base, but were unable to do further damage, as Cameron Maybin grounded into a fielder's choice that got Grandal in a rundown between third and home, and Everth Cabrera struck out to end the frame.
"We had guys on second and third with one out in a 3-1 game and couldn't get that extra run in," Black said, "and we couldn't get the two-out hit after that."
The Padres dropped to 5-46 this season when trailing after six innings.
The teams exchanged runs late, but the Friars were unable to rally. Miami center fielder Justin Ruggiano hit a solo shot to lead off the seventh, and Grandal hit a sacrifice fly in the eighth to end the scoring.
"It goes back to timely hitting," Black said. "No answer there. We had some opportunities and we didn't cash in."