Wanderers were due to play Brentford on April 27 but players refused to play the fixture over unpaid wages.
The club then controversially postponed their scheduled game against Doncaster on August 20 just 36 hours before it was due to kick off - over welfare concerns for youth players they claimed to have been forced to field after starting the season in administration.
Bolton, who began the season on minus 12 points as punishment for going into administration, have also been fined £70,000 by the EFL.
But the points penalty and half of the fine has been suspended for 18 months. The full punishments will only be activated if the club are subject to further misconduct charges for non-fulfilment of fixtures in this period.
Meanwhile in a separate development, the EFL have announced it will appeal against the decision of the independent panel.
The Rovers statement read: "Doncaster Rovers note the outcome of the independent panel’s disciplinary hearing into Bolton’s cancellation of their fixture against us and failure to fulfil a previous game against Brentford.
"Bolton pleaded guilty to the charges, with the independent panel deciding that our fixture should be rearranged along with a fine and suspended points deduction.
"We are obviously disappointed with this decision and believe it has the ability to undermine the integrity of the competition.
"We understand the EFL have the option of appealing the decision, and we believe it is prudent to await the outcome of that process before taking further action. We will look to work with our counterparts at Shrewsbury Town and Tranmere Rovers to rearrange those postponed fixtures."
In their own statement, which confirmed their decision to appeal, the EFL said: "The EFL is disappointed by conclusions reached by the independent Disciplinary Commission in respect of Bolton Wanderers and it is firm view of the League that sanction imposed is too lenient when consideration is given to all the circumstances of the case.
“Given the potential for postponements to have a significant impact on competition integrity and, following receipt of advice overnight on the reasons provided, the League will appeal the outcome in the strongest possible sense.”