But Flynn let drive a single, to the wonderment of all, And Blake, the much despised, tore the cover off the ball; And when the dust had lifted, and men saw what had occurred, There was Jimmy safe at second and Flynn a-hugging third.
To the amazement of the fans, Flynn gets a hit and runs safely to first base ("a single"). If that's not enough, Blake (not a fan favorite) also gets a hit (a double) and reaches base safely.
That expression, "tore the cover off the ball," doesn't literally mean that the ball is ruined and everyone has to go home. It's just another figurative turn to emphasize the point that Blake hit the ball really hard.
When the dust finally settles from all that running and sliding, Jimmy is standing on second base and Flynn is on third base (he ran there from first when Jimmy got his hit). Things are looking up for Mudville. Jimmy and Flynn represent the tying runs (if they both run home, it'll be 4-4) and now Casey is going to get a chance to hit after all.