The Kazakh WorldTour team had been suspended from the organisation since July when Boom took to the start line with the rest of the Astana team at the Grand Départ in Utrecht.
The Dutch rider later withdrew ahead of stage 10 due to illness.
Although not against UCI or WADA rules, the MPCC requires riders to be rested when their cortisol levels drop below recommended values.
The pressure group released a statement detailing their decision, and said that "the Board of directors of MPCC has decided to exclude Team Astana for non-compliance with the 9th article of the internal regulation".
Cortisol hormones can be administered to riders by a doctor and are permissible under the UCI's Therapeutic Use Exemption (TUEs) conditions. However, as the statement goes on to detail, "the use of that medicine has frequently been abused in the history of sports (including in cycling) for the purpose of increasing performance".
The incident with Boom follows several doping cases involving Astana riders towards end of last season including positives for the Iglinskiy brothers which put the team's WorldTour licence in jeopardy.
Thank you for reading 20 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1