The Bruins selected Subban, who played two seasons for Belleville in the Ontario Hockey League, with the No. 24 pick in Pittsburgh. Boston has no selections in the second round, scheduled for Saturday when the last six rounds will be conducted.
Thomas, who has a year left on his contract at $5 million, waived his no-trade clause last week, Bruins general manager Peter Chiarelli said Friday.
Subban, 18, was 25-14 with a 2.50 goals-against average and .923 save percentage last season when he was burdened by groin and ankle injuries. In the previous season, he had a 3.16 goals against average and .900 save percentage in 32 games.
He joins Niklas Svedberg as the two goalies added by the Bruins since the 2011 Stanley Cup champions were eliminated in the first round this year by Washington. Svedberg, 22, signed a two-year deal on May 29 after three seasons in the Swedish Elite League.