The defending World Series champions are 5-1 for the first time since 2008.
St. Louis came into the game leading the majors with nine homers. It has five in its first two games at Great American Ball Park.
Lohse (2-0) has made impressive starts in Florida's summery warmth and Cincinnati's April chill. He took a no-hitter into the eighth inning of a 4-1 win in Miami last Wednesday, allowing only one run and two hits.
With temperatures in the 40s on Tuesday night, he was sharp again, allowing Joey Votto's sacrifice fly and four hits in six innings. Jason Motte retired the side in order in the ninth for his second save in two chances.
The Cardinals rotation has been sensational so far, going 5-1 with a 1.86 ERA.
The Reds handed out another big contract before the game, giving second baseman Brandon Phillips a deal through 2017 worth $72.5 million. It came only five days after Votto got an additional 10 years and $225 million, looking to turn the 2010 NL Central champions into a consistent contender.
Phillips got a cramp in his left hamstring during a 7-1 loss to the Cardinals on Monday night and is expected to miss several days.
For the second game in a row, the Cardinals got to a Reds starter before he could break a sweat. They hit three homers in the first inning off Homer Bailey on Monday night.
Beltran hit Leake's fifth pitch into the stands in right field. Leake escaped another big Cardinals first inning by getting Yadier Molina to ground into a double play with the bases loaded. Molina also grounded into a double play with two runners aboard in the eighth.
Lance Berkman, who has the most homers by a visiting player at Great American Ball Park, tripled into the right-field corner in the sixth. Freese followed with his third homer, a drive that bounced off the top of the wall in right field and caromed up into the stands.
Berkman left the game in the eighth with tightness in his left calf.
Zack Cozart hit his second triple of the season in the bottom of the inning and scored on Votto's sacrifice fly, making it 3-1.
NOTES: LHP Jaime Garcia starts the final game of the series for St. Louis. He's 6-1 in his career against the Reds with a 3.13 ERA. He has given up more than three runs only once in his seven starts against Cincinnati. ... RHP Johnny Cueto makes his second start for Cincinnati. He pitched seven innings in a 4-0 opening win over Miami last Thursday. ... SS Rafael Furcal was out of the Cardinals' starting lineup for the first time, getting some rest. ... Reds RH reliever Nick Masset, who started the season on the 15-day DL with a sore shoulder, hasn't started throwing yet.
Link to Boxscore: St. Louis 3 at Cincinnati 1