The Imps will be gunning for revenge after their 2-1 FA Cup defeat to the Toffees earlier this year.
Other exciting fixtures include fourth tier Newport County v Premier League West Ham, and a East Midands derby face-off between Nottingham Forest and Derby County.
There are five League Two-Premier League ties in total: Crewe, Colchester and Crawley also drawn against top flight opposition (Villa, Palace and Norwich City respectively).
The ties will be played the week beginning 26 August.
Marcelo Bielsa's Leeds, who beat Salford City 3-0, face fellow Championship side Stoke.
The draw, which is split into northern and southern sections, sees the inclusion of the 13 Premier League clubs who are not competing in European competitions, as well as Championship sides Cardiff City and Fulham.
Draw in full
South section
Plymouth v Reading
Crawley v Norwich
Newport v West Ham
Oxford United v Millwall
Watford v Coventry
Swansea v Cambridge United
Cardiff v Luton
Bristol Rovers v Brighton
Crystal Palace v Colchester
Fulham v Southampton
Bournemouth v Forest Green
Southend v MK Dons
QPR v Portsmouth
North section
Crewe v Aston Villa
Lincoln v Everton
Leeds v Stoke
Sheffield United v Blackburn
Rotherham v Sheffield Wednesday or Bury
Newcastle v Leicester
Burton v Morecambe
Burnley v Sunderland
Nottingham Forest v Derby
Grimsby v Macclesfield
Preston v Hull
Rochdale v Carlisle
2-4 | ||
Harry Anderson 1' Bruno Andrade 70' | Lucas Digne 36' Gylfi Sigurdsson 59' (pen.) Alex Iwobi 81' Richarlison 88' |