Federer lost in his first match back after a ten-week break in the Mercedes Cup in Stuttgart.
World number 307 beats 18-time grand slam champion in three sets in Stuttgart.
After Roland Garros, reigning French Open champion leads Swiss by almost 3,000 points in the Race to London.
18-time Grand Slam winner missed clay-court swing but will return to action in Stuttgart on Wednesday.
Nadal and Federer have won a combined seven titles this season including two Grand Slams.
Djokovic most recently crashed out in the French Open quarter-final.
Nadal won his 10th French Open title at Roland Garros in 13 visits.
Nadal has made seven finals and won four titles thus far in 2017.
Paul Annacone, who also worked with Pete Sampras, will join Swiss' coaching team for grass-court swing.
Spaniard won his 10th French Open crowd by beating Stanislas Wawrinka.
Federer is expected to return to action at the start of the grass-court season on 14 June.
World number one faces fellow three-time major winner Stanislas Wawrinka in French Open semi-finals.
Nadal and Federer have won three titles apiece in 2017.
Federer has won 19 of his 20 matches in 2017 despite missing six months with a knee injury.
Becker also thinks either Federer or Nadal can finish the year as number one in the singles race.
Austrian is "physically and mentally" ready to challenge for grand slams believes Gunter Bresnik.
Federer will play just two events after a 10-week break leading up to Wimbledon in July.
Federer took a 10-week break following his win at the Miami Masters.
Roger Federer has won three titles and is 19-1 in 2017 so far.
Federer has won three titles - Australian Open, Indian Wells and Miami Masters - thus far in 2017.
Exclusive: The 2002 French Open winner confident his fellow Spaniard will triumph at Roland Garros.
Federer, Nadal and Djokovic together hold 44 Grand Slam titles.