Germany's Beck, who was due to take on the Swiss in the final match of day three on Hisense Arena, had to scratch after suffering a lower back injury.
Federer will now meet the winner of the clash between Croatian Ivo Karlovic and Argentinian Carlos Berlocq in the third round.
The Swiss, seeded number three in Melbourne, revealed he was unaware of Beck's injury until after practice on Wednesday morning.
"I didn't know anything about it until I saw him in the locker room and he came up to me. I was like 'hey, what's going on? Good to see you again', because he's a good friend. I've practised with him in the past in Switzerland.
"He said 'I'm not so good actually, I have a bad back'. It came as a surprise.
"He said he had a lot of painkillers during the last match. I think it happened four, five days ago. He doesn't want to risk it early in the season. I guess it's the smart decision for him to take."
The 16-time grand slam winner was adamant having an extra day off would not disrupt his momentum.
"I'll just take it easy this afternoon and come out tomorrow [Thursday] and hit intensely and then I'll be ready for the next match," he said.
Mardy Fish became the highest seed to exit the 2012 Australian Open following his defeat to Alejandro Falla.
American Fish committed 58 unforced errors to help hand his Colombian opponent a 7-6 (7/4) 6-3 7-6 (8/6) victory in exactly three hours.
Having lost the first set on a tie-break, eighth seed Fish became distracted by Falla's use of the trainer and a solitary break handed the world number 71 a two-set lead.
It looked bleak for Fish when he found himself a break down in the third, but he hit back to take it to another breaker only to again find himself on the back foot.
Falla, best known previously for squandering a two-set advantage against Federer at Wimbledon in 2010, looked nervy when wasting his first two match points, the first with a double fault.
But when a third chance presented itself he was grateful for Fish putting a backhand volley wide.
"I didn't play great and he played well," said Fish, who was irritated at Falla's repeated call for the trainer at the changeovers.
"For someone who is in the latter stages of his career and prides himself on his fitness, I don't enjoy that at all," he added.
"I have a hard time calling the trainer for anything. First of all, I wouldn't want the other guy to know that I was hurting in the first place. But to be able to get help for lack of fitness..."
In the day's other matches, 11th seed Juan Martin Del Potro beat Blaz Kavcic 6-4 7-5 6-3 and left-handed Spaniard Feliciano Lopez overcame Flavio Cipolla 7-5 7-6 (7/4) 6-2.
Seventh seed Tomas Berdych eased past diminutive Belgian Olivier Rochus 6-1 6-0 7-6 (7/4), while big-serving South African Kevin Anderson edged out Sergiy Stakhovsky 3-6 6-1 7-6 (7/3) 6-3.
16th seed John Isner spent four hours and 41 minutes on the Margaret Court Arena to grind out a tough win over David Nalbandian in the fifth set 4-6 6-3 2-6 7-6 (7/5) 10-8.
In another five set marathon match, Alexandr Dolgopolov came through against Tobias Kamke 4-6, 6-1, 6-1, 3-6, 8-6. He will play Bernard Tomic in the next round after the Australian came from a set down to beat Sam Querrey 3-6, 6-3, 7-6, 6-3.
In Wednesday's other matches Ivo Karlovic defeated Carlos Alberto Berlocq 7-6, 3-6, 6-3, 6-4 while Nicolas Almagro beat Grigor Dimitrov 4-6, 6-3, 6-7, 6-0.
Finally, in Wednesday's last game Stanislas Wawrinka overcame Marcos Baghdatis in four sets winning 7-6, 6-4, 5-7, 6-1. Wawrinka will play Almagro in the next round.
Selected men's results from Day 3 of the Australian Open
Roger Federer def. Andreas Beck (ret.)
Ivo Karlovic def Carlos Berlocq 7-6 3-6 6-3 6-4
Alejandro Falla def. Mardy Fish 7-6, 6-3, 7-6
Tomas Berdych def. Olivier Rochus 6-1, 6-0, 7-6
Juan Martin Del Potro def. Blaz Kavcic 6-4, 7-5, 6-3
Bernard Tomic def Sam Querrey 3-6, 6-3, 7-6, 6-3
Alexandr Dolgopolov def Tobias Kamke 4-6, 6-1, 6-1, 3-6, 8-6
Feliciano Lopez def. Flavio Cipolla 7-5, 7-6, 6-2
Nicolas Almagro def Grigor Dimitrov 4-6, 6-3, 6-7, 6-0
Philipp Kohlschreiber def. Pere Riba 6-0, 4-0 (ret.)
Yen-Hsun Lu def. Florent Serra 7-5, 6-2, 6-2
Kevin Anderson def. Sergiy Stakhovsky 3-6, 6-1, 7-6 , 6-3