Son was replaced by Steven Bergwijn at half-time and, asked afterwards if the South Korean could be absent 'for long', Mourinho said: "Yes. Hamstring."
Spurs can scarcely afford to be without Son for any length of time, as they continue to compete on three fronts during the congestion start to the season.
Next week, they face midweek home matches against Chelsea in the Carabao Cup fourth round and Maccabi Haifa in a Europa League play-off before a visit to Mourinho's former club Manchester United next Sunday – with Son now surely a doubt for all three fixtures.
Spurs' hopes of making it four wins on the bounce were scuppered when Newcastle were awarded a stoppage-time penalty, converted by Callum Wilson, after the ball struck Eric Dier's arm. The decision was made after referee Peter Bankes consulted with the VAR and checked the pitch-side monitor.
Newcastle boss Steve Bruce afterwards described the new handball rule, introduced by lawmakers IFAB this season, as "ludicrous" and "a nonsense" and admitted his side got lucky after his goalkeeper Karl Darlow kept Spurs at bay with a string of saves.
Mourinho refused to comment on the new law or the role of the VAR but praised Roy Hodgson, who yesterday said the new handball rule was "killing football".
"I don't want to comment, I just don't want to, I don't have a message [for the game's lawmakers]," Mourinho said.
"Mr. Roy is our boss, the man with more experience, the man with the age, the man in the Premier League I always consider the eldest one, the boss, he has the status, the knowhow, respected by everyone," he added, suggested agreement with the Crystal Palace boss.
Mourinho stormed straight down the tunnel after the referee had awarded the spot-kick but his goalkeeping coach Nuno Santos was sent off after the final whistle for remonstrating with Bankes.
In a dig at United, who were awarded a penalty after the final whistle in Saturday's win over Brighton, Mourinho said: "The only thing that I know is that I'm more experienced than [Nuno] and I left down the tunnel when the referee blew the whistle for the last time.
"I know that in some matches at some clubs, even after the last whistle, it's possible for something important to happen, but for us I knew that after the last whistle it was over for us and I left for the dressing room. So Nuno a little bit more naive than me and he stay there."
Spurs finished with 23 shots, including 12 on target, and 66 percent possession but could not capitalise on Lucas Moura's first-half goal.
"My team did a fantastic match, I cannot ask more from the players," Mourinho said. "Their goalkeeper was phenomenal. I cannot ask more from my players.
"We kept them away from the special box and we couldn't do more than what we did. The team played very very well.
"It was a very complete match, offensively and defensively. No problem defensively, we created a lot of chances. Really, really good, I'm very happy with the performance."