The 21-year-old full-back had previously been out injured and has now undergone surgery that will force him out of action for a lengthy period.
"Young Jon Flanagan, unfortunately, has just had an operation that will probably have him out for a few months - which is disappointing," Rodgers told Liverpool's official website.
"Glen Johnson should be back training over the course of the weekend."
The Spaniard has been excellent since arriving on Merseyside and Flanagan's injury seriously reduces the competition for places within the Reds' back four.
As Rodgers stated, Johnson should be back for selection soon - but Manquillo's form means the England full-back wouldn't even get a sniff currently.
|Team||Pos||Tackles Won||Interceptions Won||Effective Clearances||Aerial Duels Won||Apps||Mins|
Indeed, as Opta stats show, the 20-year-old has outperformed his rivals for a starting berth at full-back, having also played one game down the left-hand side.
Manquillo's 12 tackles won is higher than any Liverpool defender including centre-backs, while he has also proven competent in terms of clearances and in the air. Interceptions-wise, Manquillo is again very strong.
Johnson's form in his opening two games for Rodgers' side before injury simply doesn't compare.
Rodgers added: "Young Javi at right-back is only 20 years of age but he's like a rash. He's all over attackers and he's hard to beat. He gets forward well and he wants to create."
Flanagan's injury is a blow to Liverpool's squad, then, but not a total disaster when it comes to Manquillo's first-team prospects.