Bryant moved up to third place, behind former Lakers Kareem Abdul-Jabbar (38,387) and Karl Malone (36,928).
"I congratulate Kobe on reaching this milestone," Jordan told the Associated Press. "He's obviously a great player, with a strong work ethic and has an equally strong passion for the game of basketball. I've enjoyed watching his game evolve over the years, and I look forward to seeing what he accomplishes next."
Abdul-Jabbar won five championships with the Lakers and six over his career.
Malone was a Laker just for a season. Bryant recently said that his former teammate should be associated with the team he went into the Hall of Fame with, which was the Utah Jazz.
"Just because he was a Laker for one year, doesn't make him a Laker," said Coach Byron Scott earlier in the week.
Bryant won't catch Malone for some time, if at all, given he's under contract just for this season and next. If Bryant plays beyond the 2015-16 season, he'll have a real shot to finish second overall, and even catch Abdul-Jabbar.
The All-Star guard is in his 19th season, averaging 25.4 points a game this season, heading into Sunday's game against the Timberwolves.