The hosts were penalised important points from their World Test Championship tally after their epic win over New Zealand in the second Test at Trent Bridge.
Richie Richardson of the Emirates ICC Elite Panel of Match Referees imposed the sanction after England were ruled to be two overs short of the target.
England, whose points tally rose to 42 after their incredible win, now sit at the 8th spot on the World Test Championship standings with only 40 points. Their point percentage also took a hit, which fell from 25 to 23.80.
In addition, as per Article 16.11.2 of the ICC World Test Championship playing conditions, a side is penalised one point for each over short. As a result, England have been penalised two World Test Championship points from their total tally.
England players were also fined 40% of their match fee for the slow over rate, in accordance with Article 2.22 of the ICC Code of Conduct for Players and Player Support Personnel. Players are fined 20 per cent of their match fee for every over their team fails to bowl in the allotted time.
England captain Ben Stokes plead guilty to the charges levelled by on-field umpires Michael Gough and Paul Reiffel, third umpire Rod Tucker and fourth umpire Martin Saggers, and accepted the proposed sanction, so there was no need for a formal hearing.
The point deduction puts a slight dampener on what was an epic win for England on the final day. Tasked with chasing down 298 in less than three sessions on the final day, it looked at one point that England were going to play for a draw when they lost Joe Root and were 56/3 and eventually 93/4.
Ben Stokes and Jonny Bairstow steadied the ship thereafter and brought it down to needing 160 in the final session. Bairstow went absolutely berserk and smashed a ton off just 77 balls and finished with 136 off 92.
Stokes, who suffered a blow to his knee, hobbled and romped his team home with an unbeaten 70-ball 75 as England completed an improbable win by five wickets.