The Braves fell behind early, struggled at the plate and appeared confused at times in the field.
The most embarrassing moment came in the seventh inning when catcher Brian McCann threw the ball to an uncovered third base on a ball four.
"I've forgot the outs on the bases. We've forgot the outs in the field," Jones said. "We're not executing the game, not thinking about what is going on."
Reminded that this wasn't normal for a Braves team managed by Bobby Cox, Jones said: "Well, this is not like any team that Bobby has coached."
Decimated by injuries, the Braves are left to play out the final six weeks of the season with little at stake. They are 56-69 and safe from finishing last in the National League East only because of Washington's ineptitude.
The Giants hadn't won a series in Atlanta since April 1993. Now they have, taking three of four from the Braves.
Atlanta started the homestand by being swept in three games by the National League Central-leading Chicago Cubs. That was bad, but the play was worse against the Giants.
Zito (7-15) worked seven innings, giving up five hits. The left-hander walked two and struck out three.
"He was really good at keeping the ball five or six inches off the plate and getting it called," Jones said.
"This is a team that's young and struggling with its confidence. It's hard to hit with both hands wrapped around your neck. That's the way it feels when you walk up there."
Jorge Campillo put the Braves in an early hole, giving up three runs in a 37-pitch first inning. Dave Roberts led off with a triple and the Giants added three singles and a hit batsman in the inning.
Campillo settled down after that, retiring 14 straight batters until Aaron Rowand hit his 12th home run with one out in the sixth ining.
"Another bad first inning," Campillo said. "There were a lot of bloop hits, but that's the game."
Campillo (7-6) gave up four first-inning runs in a loss to the Chicago Cubs on Wednesday and has surrendered 15 earned runs in his past 18 innings. Prior to that, he had allowed no more than three runs in six consecutive starts.
Cox insisted that Campillo was the victim of circumstances.
"Bloopers are bloopers," he said in defending his starter.
The Braves had just two extra-base hits and one was a double by Campillo.
Casey Kotchman, hitting .149 since being acquired from the Los Angeles Angels for Mark Teixeira, was 0-for-4 with two strikeouts and is 1-for-25 in his past eight games.
"He's probably pressing a little bit, trying to do too much," Cox said. "He's a good first baseman and he's a good hitter. It's just a matter of time, I think, until he begins to relax."
None of the hitters on either team got any breaks as the shadows took effect. The game began at the odd time of 4:35 p.m. ET.
"It's stupid. I'll go ahead and say," Jones said.
The Braves, who open a three-game series in New York against the Mets on Tuesday night, are frustrated. There is no question about that.