Molina slammed his helmet in frustration after Gardner came down with his drive at the top of the fence with a runner on and one out in the 11th.
Derek Jeter got a standing ovation before his first at-bat, and thousands stood again when he singled, although they also roared when he took a called third strike to end the eighth against Carlos Martinez after Molina's pinpoint throw on Gardner attempting to steal.
Michael Wacha dealt with a rain delay for the fourth time in his 11 starts — total idle time of 4 hours, 52 minutes. After nine pitches the Yankees had the lead, with a walk by Gardner and a single by Jeter setting up Ellsbury's RBI single.
The first three batters reached in a two-run fifth, too, with Kelly Johnson's RBI single and Gardner's sacrifice fly putting the Yankees up 3-1.
New York rookie starter Chase Whitley was vulnerable early, too. The Cardinals needed two at-bats to tie it in the first when Matt Carpenter tripled off the right-field wall and Kolten Wong doubled, but they missed a chance for more when Wong overslid third and was caught stealing for the first time in eight attempts this season.
Whitley qualified for a win for the first time in three career starts, but left with the bases loaded and none out in the sixth before the Cardinals tied it against Preston Claiborne. Allen Craig had an RBI groundout and Jhonny Peralta followed with a sacrifice fly.
Wacha bounced back after taking a foul liner off his elbow while sitting in the dugout his last time out, giving up three runs on four hits in seven innings. He had a season-low two strikeouts, the first against Ellsbury leading off the sixth.
NOTES: In a pregame ceremony, Jeter received Stan Musial cuff links and a $10,000 check for the captain's Turn 2 Foundation. ... The Cardinals also paid tribute to their 1964 team. ... Whitley is the first Yankees pitcher to make his first three career starts on the road since Ramiro Mendoza made four in a row in 1996. ... Cardinals RHP Lance Lynn (5-2, 3.60 ERA) opposes David Phelps (1-1, 3.18) on Tuesday night. Lynn is 1-3 with a 5.08 ERA in six career interleague starts. ... Wacha hasn't permitted more than three runs in any of his starts.