Wainwright struck out six and walked none. He issued one walk in his 22 1/3 spring innings.
"I'm very comfortable working both sides of the plate with several different of my pitches, moving my ball around, sinking and cutting it," Wainwright said. "I felt good out there, and a couple guys really took some tough at-bats. Bryce Harper always takes tough at-bats. He fouled some pitches off and got my count up. Other than that, I felt good."
For the second straight start, Wainwright outdueled Nationals right-hander Gio Gonzalez, who allowed three runs (one earned) on seven hits in five innings. After a passed ball advanced runners to second and third in the first, Gonzalez allowed a two-run, two-out single to Molina.
Molina padded the St. Louis lead with an RBI single in the third, an inning that was extended by an error. Molina entered the day with three RBIs in his first 19 games played this spring.
The five-inning start was the longest of the spring for Gonzalez, who allowed a combined eight runs (five earned) on 18 hits in 18 innings.
The Cardinals used Wednesday's game to get their first look at right-hander David Aardsma, the latest reliever to enter the bullpen competition. Aardsma, who signed a Minor League contract with the Cardinals after being released by Cleveland on Friday, stranded two runners while pitching a scoreless sixth.
Caleb Ramsey hit a two-run single in the eighth for the Nationals.
Harper was ejected in the fourth inning for arguing a close play at first base.
Up next: The Cardinals wrap up Grapefruit League play on Thursday with a 12:05 p.m. CT game against the Marlins at Roger Dean Stadium on MLB.TV. Michael Wacha, who will start in Cincinnati on Wednesday, will be making his fifth start of the spring. He has allowed three runs on 10 hits in 15 1/3 innings this month. This will be his second spring start against the Marlins, who will send Brad Hand to the mound to oppose him.
Jenifer Langosch is a reporter for MLB.com. Read her blog, By Gosh, It's Langosch, and follow her on Twitter @LangoschMLB. This story was not subject to the approval of Major League Baseball or its clubs.