The beginning of the end of Rohr's career came early the 1968 season in the final innings of a 24-inning game against the Houston Astros. Entering the April 15th game as a relief pitcher in the 22nd inning and pitching through the 24th inning, he pulled a tendon in his pitching arm. After one more failed start against the Los Angeles Dodgers, he spent the remainder of the season on the disabled list or back in the minor leagues. Rohr made only one more appearance on the mound for the Mets, versus the Pittsburgh Pirates in 1969. Rohr was later unconditionally released by the Mets when a routine physical discovered a ruptured disc in his lower back, scuttling a proposed trade to the Milwaukee Brewers.
Rohr's first game was on September 19, 1967, and his last game was on September 19, 1969. He stayed with New York Mets for his entire career.