Rooney was shown a red card in the second half for protesting after Blackburn defender Joe Rankin-Costello's late header had cancelled out Michael Obafemi's first-half opener, but Whittaker headed a dramatic late winner.
Kwadwo Baah's late goal sealed Watford a 2-1 home win against Middlesbrough after Edo Kayembe had cancelled out George Edmundson's opener for the visitors.
Oxford substitute Louie Sibley's first goal for the club denied Portsmouth their first win of the season in a 1-1 draw at Fratton Park.
Mark O'Mahony headed Pompey into a second-half lead, while Elias Sorensen's early penalty for the hosts was saved.
Portsmouth boss John Mousinho later apologised to assistant referee Bhupinder Singh Gill after the game had been temporarily halted in the second half for an alleged discriminatory comment made from the stands.
Pompey also released a later statement appealing to fans for further information.
Jesurun Rak-Sakyi struck twice on his birthday as Sheffield United beat Luton 2-0 at home to move level on points with leaders Sunderland.
Crystal Palace loanee Rak-Sakyi marked his 22nd birthday with a goal in either half as the Blades extended their unbeaten league start to nine matches.
The Hatters slipped to their fifth league defeat of the season and sit one point above the relegation zone.
Burnley missed the chance to go top after they were held 0-0 at home by Preston in a bad-tempered Lancashire derby, with referee Gavin Ward brandishing seven yellow cards.
Preston's Emil Riis had an early effort disallowed for offside, which TV replays showed to be the wrong decision.
West Brom's winless league run extended to three matches as they missed the chance to go level at the top after being held 0-0 by Millwall at The Hawthorns.
Norwich maintained their climb up the table and extended their unbeaten home league run to 20 matches by thumping Hull 4-0 at Carrow Road.
Marcelino Nunez and Josh Sargent put the Canaries in control and after the latter struck a post with a second-half penalty, further goals from Liverpool loanee Kaide Gordon and Borja Sainz sealed a convincing win.
Sheffield Wednesday's Shea Charles fired a stoppage-time winner to clinch his side a 2-1 win at Coventry.
Djeidi Gassama had cancelled out Jack Rudoni's opener for Coventry before half-time and on-loan Southampton midfielder Charles struck in the third minute of added time.
Curtis Nelson and Marcus Harness scored within the space of a minute early in the second half as Derby won 2-0 at home against QPR, while Swansea were held 0-0 at home by Stoke.
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