Pronouns come in 3 persons: first, second, and third.
First-person pronouns refer to the speaker(s).
Second-person pronouns refer to the person or group being spoken to.
Third-person pronouns refer to a person or group that is not being spoken to.
If you are in the group being spoken about, a third-person pronoun cannot be used; the entire group inherits your "second-person-ness". If you are not in the group being spoken about, only one other person is available, so a third-person plural pronoun cannot be used. Therefore, "their" cannot be correct in this situation.
However, the sentence does allow for two possible pronouns, with 3 meanings:
1a: Sara and you have pens. Your pens are red.
The pens that you and Sara have are red. (This meaning would be conveyed by de-stressing "your" and stressing "pens" and "red"; the intent is to distinguish "pens that Sara and I have" from "pens that other people have.")
1b: Sara and you have pens. Your pens are red.
Sara has pens, you have pens; Sara's pens are not red, your pens are red. (This meaning would be conveyed by stressing "Your" and "red"; the intent is to distinguish "pens that Sara has" from "pens that I have".)
2: Sara and you have pens. Her pens are red.
Sara has pens, you have pens; Sara's pens are red, yours are not. The intent, again, is to distinguish "pens that Sara has" from "pens that I have".
If you have 1 pen and Sara has 1 pen, then option 1a above is the only valid choice; in option 1b and 2, the use of "pens" after the possessive pronoun requires more than one pen to belong to each person.