2nd Base tagged with glove while hole ball in hand

[BretMan]

Did the fielder touch the base before the runner did? You didn't give us that little detail and it's kind of relevent!

A tag of a base has a different criteria than a tag of a runner.

When tagging a base, the fielder may touch the base with any part of his body, or properly worn equipment, while securely holding the ball. So, catching the ball in the glove while the foot is on the bag, or touching the base with the glove while holding the ball in the bare hand are both legal tags of a base.

Tagging a runner requires actually touching the runner with the ball held securely in the hand or glove doing the touching.

As described in your sample play, the fielder has made a legal tag of the base. If he did it before the runner got there, you should have called the runner out, not safe.