Murray could not force a single break point against the top seed's service and Federer sealed the second set in 46 minutes with a sweeping forehand.
The top seed failed to earn a single break point in the match as he went out in one hour and seven minutes.
Pacific shoots 9 of 14 from 3-point range to bounce No. 2 seed Miami in the biggest upset of the round of 64.
Michigan overcame a 14-point deficit and knocked off No. 1 seed Kansas 87-85 in overtime earlier Friday night.
Sixth seed Clijsters trailed 5-2 and later faced match point in the deciding set against the Frenchwomen before a five-game rally transformed the semi-final.
That rapid ascension culminated with Quinnipiac putting together a season for the ages, rolling through a 21-game unbeaten streak at one point and into the NCAAs as the top seed.
Henman was helped by a controversial over-rule from the umpire while facing break point at 4-4 in the opening set against ninth seed Lee.
As the fourth seed he receives a bye through to the second round, at which point he will meet Marcos Baghdatis or Sam Querrey.
Looking to land a No. 1 seed in the NCAA tournament, the Hoyas squandered an early 16-point cushion against Cincinnati and fell behind briefly in the second half before clamping down with their signature defense.
It was a huge breakthrough for the fifth seed and he took full advantage by firing down an ace on his second set point to move into the lead for the first time.
Third-seed Venus had looked a nailed-on winner until the second-set tiebreak, at which point her serve inexplicably deserted her.
Zach LeDay had 13 points and 15 rebounds to lead No. 13 seed South Florida (12-19), which shot 24.2 percent and squandered an eight-point cushion down the stretch in a game between offensively challenged squads that both went 3-15 in conference play.
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