Freeman had five RBIs in the first two innings and the Braves battered Santana in his return from the disabled list, routing the sluggish New York Mets 9-3 on Saturday night.
"Unfortunately, he really didn't have command of the outside corner with his fastball and changeup," Jones said. "We put some good at-bats on him, but we had a bunch of balls that had eyes tonight."
Kris Medlen (3-1) pitched effectively into the seventh inning, striking out seven while improving to 2-0 since joining the rotation. A solid reliever most of the season, he has permitted one run in each of his three starts.
"I just take the ball and run with it," Medlen said. "I love competing. I love the chess match of starting. Relieving, if you don't have your pitches that day, you're going to get crushed. So it's two different mindsets and I like this one."
Santana (6-8) got only four outs. He was charged with eight hits -- seven singles -- and a season-high eight runs in his first outing since July 20.
The left-hander was sidelined for three weeks with a sprained right ankle, a stint on the DL also intended to refresh his surgically repaired shoulder. But he was hit hard for the fourth straight start and left trailing 6-0 after 43 pitches.
"I'm fine. It's just one of those nights I didn't execute my pitches," Santana said. "I didn't feel anything in my ankle, my shoulder, or my whole body.
"I'm just trying to get my command back. It's been a while since I faced batters of this caliber. I just need to continue to make some progress and improve my command," he added.
Freeman, who had a two-run double with two outs in the first, greeted reliever Jeremy Hefner with a three-run homer that sailed over the giant apple behind the center-field fence. The five RBIs matched Freeman's career high.
"That's as good as I can hit one," Freeman said. "I don't know how far it went, but if you guys say like 400 (feet), I'm going to be upset."
The surging Braves won for the 14th time in 17 games and sent the Mets to their 11th defeat in 12 home games. New York (54-60) has lost 21 of 29 overall to drop a season-worst six games under .500.
The 33-year-old Santana, who missed last season following major shoulder surgery, got off to a strong start this year and pitched the first no-hitter in Mets history June 1 against St. Louis. He threw a career-high 134 pitches in that game, however, and is 3-6 with a 7.98 ERA in nine starts since.
The tailspin got especially ugly after Chicago Cubs outfielder Reed Johnson, now with the Braves, stepped on Santana's foot on a play at first base July 6. Beginning with that outing, Santana is 0-4 with a 17.36 ERA in his last four starts -- by far the worst stretch of his career. He has given up 27 runs, 36 hits and six homers over 14 innings.
"I've always said that he's one of those few pitchers that hitters have to adjust to him. Maybe they have," Mets manager Terry Collins said.
Santana worked three scoreless innings in a rehab start Sunday for Class-A Brooklyn. Collins said Saturday he thought the longtime ace might be rusty, but he expected Santana would be able to finish the season strong.
He struck out Jason Heyward and Jones with two on in the first, flashing a 90 mph fastball and a useful slider. But his signature changeup was missing and the Braves took advantage on a humid, 84-degree night at Citi Field.
Freeman stroked a two-run double past a diving Ike Davis at first base to put Atlanta ahead. Dan Uggla, who is 1 for 21 with 12 strikeouts against Santana, drew a leadoff walk in the second and went to third when Paul Janish flared a soft single to center.
Medlen poked a ground ball single through a drawn-in infield for his first RBI this season and Bourn cracked a run-scoring single to right-center. One out later, Heyward and Jones hit consecutive RBI singles to finish Santana, who never really looked comfortable on the mound.
"I don't see a major difference in him. There's nothing that's way off," Bourn said. "Sometimes the opposing side is better."
Santana tossed a ball to the third base umpire and trudged off the field to scattered boos. Sitting alone at the end of the bench, he wiped his face with a towel before Collins sat down beside him for a chat.
It was the second straight start and third one this season in which Santana was knocked out so quickly he never even got to bat. He also lasted only 1 1/3 innings in his third outing of the year April 17 at Atlanta. In that game, he allowed six runs -- four earned -- and four hits.
Atlanta has won Medlen's last 14 starts dating to May 29, 2010. ... Jones (back) and Braves C Brian McCann (right shoulder) returned to the lineup. ... RHP Ben Sheets (4-1, 1.41 ERA) is scheduled to make his sixth start for the Braves when they go for a three-game sweep Sunday night. LHP Jonathon Niese (8-6, 3.82) pitches for the Mets. ... Braves RHP Tommy Hanson, on the 15-day DL since July 31 with a strained lower back, is scheduled to throw a maximum of 80 pitches Sunday in a rehab outing for Triple-A Gwinnett. That puts him on track to return to Atlanta's rotation next weekend against the Los Angeles Dodgers. ... Santana is 1-4 with an 8.39 ERA in his last six starts against the Braves.