I haven't done it yet. And the only way I know how is dependent upon having a player in your Hall of Fame already. (So you'd have to elect someone to your Hall of Fame first)
#1 Go to your team's hall of fame page
#2 Click on a player
#3 The option to retire jersey number will be there underlined, following the flag & career games played.
(http://www.buzzerbeater.com/player/6494392/hofplayer.aspx...)Example of a Hall of Fame page... in the middle of the page there's a USA flag & 95 Career Games (in bold). Next to that is where the "Retire a Jersey Number" option will be for your players.