NEW YORK—As if trying to remind himself and everyone else where he’s been and where he’s quite certain he’ll return, Roger Federer thrust his right fist overhead and pointed skyward with his index finger.

The universal gesture for No. 1.

As Federer made that signal, the 1970s song “Still the One” by Orleans rang out through Arthur Ashe Stadium on Sunday, marking the end of the four-time defending champion’s 6-3, 6-3, 6-2 victory over 28th-seeded Radek Stepanek in the U.S. Open’s third round.

Actually, for the first time in a while, Federer is not No. 1—in th...

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