Since I have a great memory and access to the internet I quickly found a case of the child of a mighty noble and a peasant becoming his father's successor, but unfortunately they don't seem to have been married.
Oldrich, Duke of Bohemia 1012-1033 and 1033-1042 apparently had no surviving children with his unnamed wife, but had his son and heir with his mistress Bozena (d. 1052), daughter of Kresina. Bozena is said to have been a peasant. And Wikipedia claims that Bozena became Oldrich's second wife. Their son Duke Bretislav I (died 1055) was the ancestor of later generations of Bohemian rulers.
Fredegund (died 597), the notorius queen and widow of King Chilperic I, Frankish king of Soissons, was said to be of lowly birth.
Fredegund was born into a low-ranking family but gained power through her association with King Chilperic.1 Originally a servant of Chilperic's first wife Audovera, Fredegund won Chilperic's affection and persuaded him to put Audovera in a convent and divorce her. Gregory of Tours remarks that Fredegund brought with her a handsome dowry, incurring the immediate affection of King Chilperic.2
Of course it is unknown if Fredegund's family was low enough in status to make her a peasant.
Emperor Romanus II (938/39-963), ruled 959-963, married 2nd, 957, Anastasia/Theofano, daughter of Krateros, a poor tavern keeper from the Sparta region of Greece, who was the mother of his three children. Of course it isn't known if her original home was rural enough for her to be called a peasant.
These are some examples I could think of and find of medieval nobles' wives of lowly birth, though two of them were wives of monarch's.