Eckstein's 12th-inning double drove in Nick Hundley, and the San Diego Padres recovered after blowing a ninth-inning lead to beat the Atlanta Braves 2-1 on Tuesday night.
"I was just trying to put the ball in play," Eckstein said. "I was able to find a hole."
Latos gave up only two hits in seven scoreless innings.
"We know we have a team that's out of contention, but we still go at them," Latos said.
The Braves wasted a chance to gain a game on NL East-leading Philadelphia, which lost to Pittsburgh.
"Anytime you lose a game like this, especially against a team that's at the bottom of their division, it's really tough," said Atlanta's Jair Jurrjens, who gave up one run in 7 2/3 innings. "We lost a game we needed to win."
Hundley led off the 12th with a double to left field off Kris Medlen (3-4). After Tony Gwynn Jr. struck out, pinch-hitter Luis Rodriguez walked. Everth Cabrera, who was 0 for 6, struck out for the third time before Eckstein delivered the go-ahead double to left-center to drive in Hundley from second.
"That's a tough one to lose as good as our pitching was," said Braves manager Bobby Cox. "They matched our pitching."
Joe Thatcher (1-0) pitched 1 1/3 scoreless innings for the win and Edward Mujica earned his second save by retiring the Braves in order in the 12th.
Adrian Gonzalez's third-inning homer, his 34th, gave San Diego a 1-0 lead that held until the ninth.
Latos and Luke Gregerson shut out Atlanta through eight innings, but Heath Bell couldn't hold a 1-0 lead in the ninth. It was Bell's third blown save in 33 chances.
Bell gave up a one-out single to Brian McCann and walked Garret Anderson before striking out Yunel Escobar. Adam LaRoche hit a two-out single to right, just in front of the reach of a diving Will Venable, to drive in pinch-runner Reid Gorecki from second base with the tying run.
Latos retired Atlanta's first 13 batters before Anderson's single to right with one out in the fifth. Latos responded by striking out Escobar and LaRoche.
Latos was 0-2 with a 14.09 ERA in his last two starts.
"That was the most important start I've had, after two bad outings," Latos said.
Latos threw only 89 pitches in seven innings but didn't get a chance to pitch the eighth.
"I thought that was enough," said Padres manager Bud Black.
The Braves loaded the bases but couldn't score in the eighth and 10th innings.
Cox called the loss "a night of missed opportunities."
"We couldn't have played a better game, couldn't have pitched any better," Cox said. "We just didn't get the hit when it meant something."
Jurrjens gave up five hits and one run with four walks with seven strikeouts in 7 2/3 innings. ... Martin Prado (headaches) and Anderson (sore back) returned to the lineup for Atlanta. ... Cox said no final decision has been made on surgery for OF Jordan Schafer's left wrist. Schafer, who opened the season as Atlanta's starter in center field, was sent to Triple-A Gwinnett on June 2. ... San Diego placed RHP Mike Adams on the 15-day DL with a right shoulder strain. OF Drew Macias will be recalled from Triple-A Portland in time for Wednesday's game. ... RHP Adam Russell, one of four pitchers obtained from the Chicago White Sox for ace Jake Peavy on July 31, joined the Padres on Tuesday. Russell was called up when RHP Cesar Carrillo was optioned to Portland.