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Skipper Johnnie Jackson also fired home for the Addicks as they saw off a second-half fightback from the visitors courtesy of substitute Tom Hopper's header.
Following early Scunthorpe dominance, it was Charlton who took the lead through a sublime left-foot strike from Lookman as the first-half substitute converted his fourth goal of the season in style.
The hosts doubled their lead six minutes later courtesy of Jackson's fine low finish.
The visitors managed to pull a goal back seven minutes into the second half as Hopper headed home from a Josh Morris corner.
The Iron nearly levelled moments later but defender Charlie Goode saw his shot deflected onto the post before Kevin Van Veen's follow-up was denied by Declan Rudd.
It was the 1947 winners who sealed their place in the next round as Lookman fired past Daniels from close range in the 83rd minute.
Report supplied by the Press Association.
Match ends, Charlton Athletic 3, Scunthorpe United 1.
Second Half ends, Charlton Athletic 3, Scunthorpe United 1.
Foul by Josh Morris (Scunthorpe United).
Fredrik Ulvestad (Charlton Athletic) wins a free kick in the attacking half.
Attempt missed. Lee Novak (Charlton Athletic) right footed shot from outside the box is close, but misses to the left.
Tom Hopper (Scunthorpe United) wins a free kick on the left wing.
Foul by Patrick Bauer (Charlton Athletic).
Foul by Murray Wallace (Scunthorpe United).
Lee Novak (Charlton Athletic) wins a free kick on the left wing.
Luke Williams (Scunthorpe United) is shown the yellow card for a bad foul.
Foul by Luke Williams (Scunthorpe United).
Ademola Lookman (Charlton Athletic) wins a free kick in the attacking half.
Substitution, Charlton Athletic. Jordan Botaka replaces Johnnie Jackson.
Attempt missed. Ademola Lookman (Charlton Athletic) left footed shot from a difficult angle on the left is close, but misses to the left.
Attempt blocked. Josh Magennis (Charlton Athletic) right footed shot from outside the box is blocked.
Goal!  Charlton Athletic 3, Scunthorpe United 1. Ademola Lookman (Charlton Athletic) left footed shot from the centre of the box to the bottom left corner. Assisted by Fredrik Ulvestad.
Attempt saved. Luke Williams (Scunthorpe United) right footed shot from outside the box is saved in the centre of the goal.
Attempt blocked. Luke Williams (Scunthorpe United) right footed shot from the left side of the box is blocked.
Conor Townsend (Scunthorpe United) is shown the yellow card for hand ball.
Hand ball by Conor Townsend (Scunthorpe United).
Foul by Tom Hopper (Scunthorpe United).
Patrick Bauer (Charlton Athletic) wins a free kick in the defensive half.
Corner,  Scunthorpe United. Conceded by Johnnie Jackson.
Substitution, Scunthorpe United. Sam Mantom replaces Richard Smallwood.
Attempt missed. Josh Morris (Scunthorpe United) left footed shot from the right side of the box is close, but misses to the left.
Substitution, Charlton Athletic. Lee Novak replaces Nicky Ajose.
Kevin van Veen (Scunthorpe United) is shown the yellow card for a bad foul.
Foul by Kevin van Veen (Scunthorpe United).
Fredrik Ulvestad (Charlton Athletic) wins a free kick in the attacking half.
Attempt saved. Johnnie Jackson (Charlton Athletic) header from the centre of the box is saved in the bottom right corner.
Attempt blocked. Kevin van Veen (Scunthorpe United) left footed shot from outside the box is blocked.
Stephen Dawson (Scunthorpe United) wins a free kick in the attacking half.
Foul by Josh Magennis (Charlton Athletic).
Attempt missed. Luke Williams (Scunthorpe United) right footed shot from the centre of the box misses to the right.
Attempt saved. Luke Williams (Scunthorpe United) right footed shot from the centre of the box is saved in the bottom right corner.
Substitution, Scunthorpe United. Luke Williams replaces Duane Holmes.
Hand ball by Ademola Lookman (Charlton Athletic).
Foul by Kevin van Veen (Scunthorpe United).
Ezri Konsa Ngoyo (Charlton Athletic) wins a free kick on the right wing.
Attempt saved. Josh Magennis (Charlton Athletic) right footed shot from the centre of the box is saved in the centre of the goal.

Sum: Ademola Lookman's double secured Charlton's progression into the second round of the FA Cup after victory over League One rivals Scunthorpe.


Caterham have re-entered under the company name of 1 Malaysia Racing Sdn Bhd, which owns the team's F1 rights.
Marussia have re-branded and will be known as Manor F1 Team if they return.
Both teams were given dispensation to miss last week's US Grand Prix and this weekend's Brazilian GP. The season ends in Abu Dhabi on 23 November.
Under the regulations of motorsport's world governing body, the FIA, entry fees to compete next year must be paid by 30 November.
Entering on the 2015 list, even provisionally, gives both teams a greater chance of securing a prospective buyer in the meantime.
Caterham's administrators, meanwhile, expect the team to be in a position to race in the season-ending Abu Dhabi Grand Prix.
"I think I've got enough confidence now to say I'd be very surprised if we were not racing in Abu Dhabi," said Finbarr O'Connell, one of Caterham's co-administrators representing Smith & Williamson.
"I'm now really hopeful for the future of the team."

Sum:
Caterham and Marussia have both been included on next year's entry list for the Formula 1 world championship despite going into administration.