In "A Poison Tree," this line literally means that the enemy snuck into the speaker's garden. The word "stole," for example, means to sneak or creep into a place. However, there is also a deeper meaning here: by using the word "stole," a word suggestive of stealing or theft, the speaker implies that the enemy entered without his permission. So, in one respect, the enemy is like a thief or a criminal.

In the next line, the reader learns how the enemy was able to sneak into the speaker's garden:

When the night have veiled the pole.

So, the enemy entered the garden at night, using the cover of darkness as a sort of protection against being detected by the speaker. In fact, it was so dark that night that the "pole," a reference to the North Star, could not be seen. Thus, the night sky helped to camouflage the enemy.

Literally, the persona's enemy "stole" into the garden, which means "crept" or "sneaked" in quietly. Literally, therefore, this line means the enemy sneaks into the persona's garden. We also learn that it is very dark outside, for the poem says "when the night had veiled the pole." The "pole" most likely refers to the star Polaris, the North star, which is perhaps on this particular night obscured by clouds. 

However, "stole" is, beyond its literal meaning, also a double entendre, a word with more than one meaning. Stole does mean creep or sneak and literally the enemy sneaks in. But stole also is the past tense for steal in the sense of rob, so there is a suggestion or connotation of the enemy not only creeping in but creeping in illicitly to steal.