Choo hit solo homers in the fourth and sixth inning, giving him nine this season. The multihomer game was his second in eight days and ninth of his career.
Mike Leake (3-2) went 6 2-3 innings and pitched around nine hits. The Marlins had 14 baserunners but stranded 12 and hit into two double plays.
That gave the crowd of 14,866 little to cheer about, and the biggest roars came when highlights of the Miami Heat's playoff victory over the Chicago Bulls two miles away were shown on the video scoreboard.
The Marlins were shut out for the seventh time, most in the majors. Cincinnati climbed a season-high eight games above .500 and improved to 5-1 against Miami, which has lost four in a row.
The Marlins fell to 0-10 this year with the retractable roof open in their stadium. The ball carries better in those conditions, and Choo twice sent it flying off Alex Sanabia (2-6).
Choo homered into the nightclub beyond the left-field fence, then pulled a homer into the Marlins' bullpen in right field. He also led off the game with a single and scored on a double by NL RBI leader Brandon Phillips.
Choo's four hits tied a career high, and he raised his average to .322. Joey Votto added two hits and an RBI for the Reds, who improved to 20-6 when they score first.
They led 4-0 in the seventh when Miami mounted a threat. With runners at second and third, Sean Marshall came on and struck out Derek Dietrich with a 3-2 curve to end the inning.
Miami put two runners aboard again in the ninth. Aroldis Chapman then threw seven fastballs of at least 100 mph to Dietrich, who finally struck out looking on a changeup.
The Marlins managed three infield hits among their 10 singles but went 1 for 10 with runners in scoring position. They rank last in the majors in wins at home, where they're 5-13.
Sanabia allowed four runs in six innings and has lost five consecutive starts.
Notes: Cincinnati 3B Todd Frazier, batting .229, was given the night off. ... Reds starters have allowed one earned run in 22 1-3 innings over the past three games. ... Cincinnati RHP Mat Latos will try to win his fifth consecutive decision in the series finale Thursday against rookie Jose Fernandez.