The 52-year-old was dismissed with the club second in the SPFL Championship table, but having slipped into a spell of indifferent form. Fans had called for Brown to be removed in the wake of a 1-1 draw with Alloa Athletic on Saturday.
The decision to appoint the former Dundee midfielder as manager last February had not been met with the universal approval of supporters but he would gain some credit for his part in the club's stirring, if unsuccessful, attempt to avoid relegation from the top flight.
The Dens Park side were expected to be more persuasive in the pursuit of promotion this season - Brown last month signed the likes of former Rangers midfielder Stephen Hughes and former Hearts forward Christian Nade - and concerns over the team's form have caused the Dens Park board to act. The draw with Alloa left Dundee with just one win from four matches and allowed Falkirk to stay ahead in the table on goal difference.
It is understood that Hartley - who resigned as Alloa manager last month - is now the board's preferred candidate to take over and his appointment could be confirmed as early as today. While at Recreation Park, the former Scotland internationalist led the part-time side to two consecutive league titles and has intimated already that he wants to take charge of a full-time club.
If Hartley is appointed then his first match will be against title rivals Hamilton Academical on Saturday, a crucial fixture which likely forced the hands of Dundee directors in choosing to sack Brown. A club statement last night read: "Dundee and John Brown have today announced they are to part company by mutual agreement.
"The club agreed with John's expressed view that, after recent results, this is the best way forward. John stated that he has loved his time at Dundee as a player and a manager. He still passionately wants Dundee to win the league this season and would share in our pride if we go on to do so.
"The board of directors would like to put on record their thanks not only for his valiant efforts in attempting to keep us in the Premier League last season when no-one gave us a chance, but also for his hard work and diligence in achieving the current points total which sees the club joint top of the league with 14 games of the season to go.
"The club expects to move quickly to appoint a new manager to continue the good work by the management and players to date and to and get us over the line as champions in May.
"We urge the fans to continue to support the club in the superb numbers they have done so far this season."