On May 2, 2012, Popovich won his second Coach of the Year Award for the 2011–12 NBA season.
On November 29, 2012, Popovich sat out starters Tim Duncan, Tony Parker, Manu Ginóbili, and Danny Green for a nationally televised game against the Miami Heat. Popovich has frequently sat out his starters on road trips over the years to ensure they have enough rest for the playoffs; the Spurs' roster was among the oldest in the league. NBA commissioner David Stern was outraged by this and said on the night of the game that it was "unacceptable," and "substantial sanctions [would] be forthcoming." On November 30, Stern fined the Spurs $250,000 for what he called "a disservice to the league and the fans." According to Stern, Popovich had not informed the Heat, the league or the media in a suitable time frame that the four players were not making the trip to Miami. Stern's decision was criticized by commentators such as Adrian Wojnarowski of Yahoo! Sports, who said, "Stern doesn't care about the realities of his league, just the appearances. To him, the appearance on Thursday night was that Popovich had tried to embarrass him on national television and that's why the commissioner tossed that tantrum."