Farrell, a second-half replacement at the Kobe Misaki Stadium, was attempting to pick the ball up off the ground in the 70th minute when he was struck by a shoulder-led charge by flanker John Quill that caught him on the jaw.
The England captain crashed to the floor but was quickly back on his feet as a brawl erupted with Mark Wilson leading the shoving before being joined by a large group of his outraged team-mates.
Referee Nic Berry reviewed the footage and dismissed Quill, who could have no complaints at being severely punished.
Eddie Jones predicted that playing the USA would be like facing “15 Donald Trumps – aggressive, brash, ready to take on the world”, but the biggest challenge was dealing with the suffocating humidity in Kobe.
With the roof to the ground closed, the stifling conditions made for an energy-sapping encounter. Winger Joe Cokanasiga plundered two tries and it was a more accomplished display than the underwhelming victory over Tonga that opened Pool C, producing a second successive bonus-point win.
England’s set-piece battered Gary Gold’s underdogs in the first half before they cut loose, expertly directed by fly-half George Ford who was named man of the match.
The set-piece dominance England enjoyed was helped early on when Eagles prop David Ainuu was helped early on from the pitch after falling awkwardly at a scrum.
A muscular run from Billy Vunipola sucked in defenders to create space that was exploited by Ford in the next phase by running through a large gap.
The kicking game superbly directed by Ford and Willi Heinz was serving England well but their discipline was far less on point after conceding four penalties inside 15 minutes.
A driving line-out sent the USA hurtling backwards so when England were awarded a penalty in front of the posts, Ford opted for touch instead of taking the points and was immediately rewarded. Once again the Eagles were scattered at the set-piece and Vunipola was at the bottom of the pile of white shirts as the pack crashed over.
Just as their line-out was dismantled, England pulverised the underdogs’ scrum and from the ensuing penalty they launched another arrowing line-out that ended with Luke Cowan-Dickie touching down.
The bonus point arrived in the 47th minute when Joseph created the opportunity for Cokanasiga to drive over.
Wilson, who had replaced Vunipola at half-time, made a series of purposeful carries and wing Ruaridh McConnochie was the next to cross as the beneficiary of some quick hands.
Ford produced a neat step to enable Lewis Ludlam to cross before Quill was sent packing.
Cokanasiga went over for his second try but the USA grabbed a late consolation score through replacement Bryce Campbell as England were caught on the counter-attack.
England: Daly, McConnochie, Joseph, Francis, Cokanasiga, Ford, Heinz, Marler, Cowan-Dickie, Cole, Launchbury, Kruis, Curry, Ludlam, B. Vunipola. Replacements: Farrell for Francis (50), Youngs for Heinz (50), Genge for Marler (41), Singleton for Cowan-Dickie (69), Sinckler for Cole (41), Lawes for Launchbury (50), Wilson for B. Vunipola (41). Not Used: Watson.
USA: Hooley, Scully, Brache, Lasike, Iosefo, MacGinty, Davies, Ainuu, Taufete’e, Lamositele, Landry, Civetta, Lamborn, Quill, Dolan. Replacements: Te’o for Hooley (43), Campbell for Lasike (61), de Haas for Davies (50), Kilifi for Ainuu (3), Mullen for Lamositele (43), Peterson for Civetta (50). Not Used: Fawsitt, Germishuys.