The defeat meant Boro had lost 14 of their past 18 games, which has seen them fall from a play-off place down to 15th in the table.
Saturday's 4-0 win over promotion-chasing Sheffield United hinted at a change in the club's on-field fortunes but the loss against the Shakers - who went into the game bottom of the table - forced the club's board to act.
Chairman Phil Wallace told the club's official website: "It's always difficult when you have to replace the man in charge. Gary has done his best but the performances and results over the past few months have been worrying in the extreme.
"After a very promising start with a new squad, we have slipped alarmingly and the board are concerned that the present management team may be unable to deliver the club's vision of increasing attendances and developing players in a winning environment.
"We have waited longer than most others in similar circumstances, but we cannot in all good conscience continue to watch this downward spiral and do nothing.
"It's time for a change and we'll see who applies for the position. Meanwhile I'm indebted to skipper Mark Roberts who will, once again, step up and take charge whilst our search takes place."
Smith joined Boro in January 2012 and led the club to a play-off semi-final, where they were beaten by Sheffield United.
Stevenage lost just one of their first 14 games this season but after a 4-0 defeat to Swindon in October the club have won just six of their 24 matches.
Roberts had a spell as player-caretaker manager last season, prior to Smith's appointment.
Source: PA
Source: PA