MK Dons secured a 3-0 win over Northampton thanks to two penalties from Ben Reeves and Simon Church and a goal from open play from Josh Murphy.
Chelsea will now play MK Dons for the first time in a competitive fixture on Sunday 31 January at stadium:mk on Sunday 31 January, with kick-off expected at 4pm.
Meanwhile, Aston Villa avoided FA Cup embarrassment after beating fourth-tier Wycombe at the second attempt, winning a replay 2-0 to reach the fourth round on Tuesday.
However, it took Villa 75 minutes to find a breakthrough against a team from England's lowest professional league, with Ciaran Clark heading the Premier League's bottom side in front.
Villa's passage to a meeting with Manchester City at the end of the month was not smoothed until Idrissa Gana netted his first goal for the club in the 90th.
West Bromwich Albion also won their third-round replay as Salomon Rondon scored early in the second half to clinch a 1-0 win over second-tier Bristol City and a home match next against fourth-tier Peterborough.
There are no non-league teams remaining in the competition after Eastleigh lost 3-2 at second-tier Bolton.
