The 6-foot-9 Isner served 11 aces, seven of those in the second set, but was broken twice by the mercurial Russian. Safin had nine aces and faced only one break point, at 30-40 after a double-fault in the final game of the match.
Safin, 28, the No. 5 seed in this 28-player ATP Tour event, started the season with a five-match losing streak and dropped from No. 57 to No. 93 before reversing the trend by reaching the quarterfinals of a tournament at Munich, Germany, in late April.
Safin, who is ranked No. 44 this week, was a semifinalist at Wimbledon, where he beat No. 3 Novak Djokovic and No. 9 Stanislas Wawrinka before losing to No. 1 Roger Federer.
Safin improved to 3-7 on hard courts this year and will face American left-hander Wayne Odesnik in the second round. Odesnik, 103rd in the rankings, advanced with a 3-6, 6-1, 6-4 win over countryman Bobby Reynolds earlier Tuesday.
In other early matches, American Vincent Spadea beat Sebastien Grosjean of France 6-3, 3-6, 6-3; Dusan Vemic of Serbia outlasted Sam Warburg of the U.S. 3-6, 7-6 (5), 6-4; and qualifier Andrea Stoppini of Italy, ranked No. 221, ousted Igor Kunitsyn of Russia 6-1, 6-3.
Stoppini's win over the 87th-ranked Kunitsyn highlighted a day in which, with the exception of the Safin-Isner match, the lower-ranked player won.
Frei: “You learn from victories and defeats!”
Safin rebounds at Swedish Open