Whittaker’s 82nd-minute effort handed bottom-of-the-table Argyle, with new boss Miron Muslic looking on, a 1-0 win at the Gtech Community Stadium to extend their unbeaten run since Rooney’s departure to three games.
Dango Ouattara’s double helped ease Bournemouth to a 5-1 over West Brom with Jason Kluivert, Antoine Semenyo and substitute Daniel Jebbison also scoring after Caleb Taylor had headed the visitors in front.
Jamie Vardy celebrated his 38th birthday with a successful penalty as top-flight Leicester routed QPR 6-2.
James Justin’s double, coupled with goals from Stephy Mavididi, Facundo Buonanotte, Vardy and Wout Faes, sent the hosts through, although Jonathan Varane and Rayan Kolli briefly dragged it back to 3-2.
Goals from Ryan Yates and Ramon Sosa saw high-flying Nottingham Forest progress with the minimum of fuss despite making 11 changes courtesy of a 2-0 home win over Luton.
Georginio Rutter helped himself to a double before Julio Enciso and substitute Solly March wrapped up a comfortable 4-0 win for Brighton at Norwich.
Rayan Ait-Nouri and Rodrigo Gomes fired Premier League Wolves to a 2-1 win at Bristol City, for whom Scott Twine replied with a superb free-kick, while Andreas Weimann scored the only goal to give Blackburn a 1-0 win at Sky Bet Championship rivals Middlesbrough.
Winger Ayumu Yokoyama scored League One leaders Birmingham’s fastest FA Cup goal as they beat Lincoln 2-1, Lyndon Dykes doubling their advantage before Jovon Makama converted a stoppage time penalty.
Two goals from Demetri Mitchell and a third from Vincent Harper saw League One Exeter reach round four for the first time in 44 years after a 3-1 win over Championship Oxford. The visitors led through Matt Phillips’ goal but finished with 10 men after Tyler Goodrham was sent off nine minutes from time.