Pour the red wine and vinaigrette into a resealable plastic bag. Sprinkle the chicken breasts with salt and pepper, and place into the bag. Coat the chicken with the marinade, squeeze out excess air, and seal the bag. Marinate in the refrigerator for at least 1 hour.

Pour the marinade into a skillet over high-medium heat, and cook, stirring frequently, until the marinade begins to reduce and the oil separates, about 15 minutes. Place the chicken into the skillet and brown on both sides, about 4 minutes per side. Stir in the shallots, and cook, stirring, until translucent, about 10 minutes. Stir in the thyme leaves and cook until the sauce is reduced and the chicken is browned and no longer pink in the center, about 4 to 5 minutes.