The Swiss moved up four places to highlight his resurgence, having started the year with success at the Australian Open before Monday's (AEDT) 6-4 7-5 win against Wawrinka.
It had appeared as though the former world number one's career was winding down after he endured four seasons without adding to his tally of 17 grand slams, but his exploits in Melbourne marked a return to form that shows no sign of slowing down.
Though Andy Murray and Novak Djokovic – who will miss the Miami Open through injury – continue to lead the way, with Wawrinka third, Federer is the man gaining ground.
It is his highest position in the standings since October last year, when he resided in seventh.
Elsewhere in the rankings, Indian Wells semi-finalist Pablo Carreno Busta broke into the top 20 for the first time.