Prior to taking on the defending champion Miami Heat on Thursday, San Antonio Coach Gregg Popovich told Tim Duncan, Manu Ginobili, Tony Parker and Danny Green they could go home rather than traveling to south Florida.
Despite the absence of those players, San Antonio owned a six-point lead over Miami with 3 minutes to go before letting the game slip away.
The six games on the road were played in a span of only nine days and San Antonio won the first five contests of the season-long trip. Miami had not played for four days prior to meeting the Spurs.
Before the Thursday game Stern said the fact the four players were made unavailable was "unacceptable" and that "substantial sanctions" would be forthcoming.
In announcing the fine Friday Stern said the Spurs' actions were "contrary to the best interests of the NBA."
"The result here is dictated by the totality of the facts in this case," Stern said in a statement. "The Spurs decided to make four of their top players unavailable for an early-season game that was the team's only regular-season visit to Miami.
"The team also did this without informing the Heat, the media, or the league office in a timely way. Under these circumstances, I have concluded that the Spurs did a disservice to the league and our fans."
Popovich often rested key players late last season without drawing the wrath of the league office.