Gee gave up one hit in four innings but did not return following a rain delay of 1 hour, 11 minutes. The delay cost Gee, who is 7-0, a chance to become the first Mets rookie to win his first eight decisions.
The Mets have won nine of 13, including the first two games of the series.
D.J. Carrasco replaced Gee and pitched two perfect innings. Bobby Parnell (1-1) struck out five in two scoreless innings before Francisco Rodriguez completed the shutout with a perfect ninth inning.
Gee and the Mets led 3-0 when heavy wind, rain and lightning forced play to be stopped in the top of the fifth inning. The start of the game had been delayed 1:22 by another storm which brought hail to Turner Field. There was more lightning following the second delay.
The left-handed hitting Pagan pulled a two-run homer off Tim Hudson in the fourth. Pagan lofted the drive into the gusty wind blowing toward right field. The fly ball remained fair before tucking around the foul pole.
Jason Bay, who had been hitting only .067 (2 for 30) in June, had two hits following a vote of confidence from manager Terry Collins before the game.
"I'm trying to get the guy going," Collins said of Bay. "You've got to have some confidence on the field.
"When he gets his stroke back, he's the left fielder. Hands down."
Bay sat out the Mets' 4-3 win in Tuesday night's series opener.
Jose Reyes had a double and scored in the first and drove in Lucas Duda with a groundout in the seventh.
The Braves lost their third straight to fall 5 games behind the Phillies in the NL East. Philadelphia swept a doubleheader from Florida.
Hudson (5-6) gave up four hits and three runs, two earned, in four innings and has lost four of his last five decisions.
Alex Gonzalez doubled with two outs in the second and pinch-hitter Brooks Conrad had a single off Parnell in the eighth for the Braves' only hits.
Braves right fielder Jason Heyward was 0 for 2 with a walk in his return from the disabled list. He missed 18 games with inflammation in his right shoulder.
Heyward had a throwing error after fielding Reyes' double to open the game, allowing him to advance to third. Reyes scored on Ruben Tejada's groundout.
NOTES: The Braves optioned OF Matt Young to Triple-A Gwinnett to clear a roster spot for Heyward. ... OF Nate McLouth, recovering from a left oblique strain, took batting practice and expects to begin a rehab stint with Gwinnett on Thursday. ... 1B Freddie Freeman missed his second straight start with a mild right oblique strain. He said he expects to play Thursday.