The League One bottom side, who began the season on minus 12 points as punishment for going into administration, have also been fined £70,000 by the EFL.
Both the five-point penalty and half of the fine will be 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.
A statement from the EFL read: "An independent disciplinary commission, appointed under EFL regulations, has ruled that Bolton Wanderers will be handed a sanction of five points, suspended for 18 months, and a financial penalty as a result of being deemed guilty of breaching EFL regulations in failing to meet its fixture obligations."
Bolton fell into financial difficulties before the end of last season, when they were in the Championship, and cancelled a game against Brentford.
After being relegated, they were then forced to postpone a game against Doncaster earlier this season as the club tried to complete a takeover.
The club were hit with a two-point deduction for the Brentford fixture and a three-point deduction for the Doncaster game, which will now be rearranged.
The fines of £20,000 and £50,000 are for the Brentford and Donacaster games respectively.
The club have the right to appeal but, after pleading guilty to the charges, have indicated they are pleased with the outcome.
Chairman Sharon Brittan said: "We acknowledge the decision made by the panel and are pleased that these matters, which occurred under the previous administrations of the club, have now been resolved.
"Our collective attention must now be fully focused on (manager) Keith Hill, his staff and players as we look to get as many points as we can to climb the Sky Bet League One table.
"Bolton Wanderers supporters and staff have shown tremendous patience and passion throughout and we are now looking forward to working together to continue the rebuilding of this great football club."
Bolton remain bottom of the table following their punishment but have at least wiped out the 12-point deduction and have one point after three successive wins. They are are 12 points off safety and travel to Accrington on Saturday.
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