Swiss second seed Federer made it 15 straight wins over Ferrer with a 6-3 4-6 6-3 victory against the Spaniard in their Toronto quarter-final.
Federer battled during the deciding set of the ATP 1000 event but still managed to clinch the only break of serve.
The 2004 and 2006 champion saved a break point in the fifth game before taking a 4-2 lead and fighting to consolidate.
For the 15th time in their careers, Federer proved too good for the fifth seed as he reached the semi-finals on his 33rd birthday.
Awaiting him is another Spaniard in Feliciano Lopez, who upset local favourite and sixth seed Milos Raonic 6-4 6-7 (5-7) 6-3.
Raonic, runner-up last year, served 18 aces, but he was left to lament several missed opportunities in the third set.
A marathon fifth game saw Raonic waste nine break points and Lopez got the break in the eighth for his win.
On the other side of the draw, French 13th seed Tsonga continued his upset run to set up a meeting with Grigor Dimitrov.
Tsonga overcame British eighth seed Murray 7-6 (7-5) 4-6 6-4, having beaten world number one Novak Djokovic in the third round.
Dimitrov, the Bulgarian seventh seed, was fortunate to beat South African Kevin Anderson 5-7 7-5 7-6 (8-6).
Anderson had match points during the third set, only to produce three unforced errors on his stronger forehand side.
Dimitrov made him pay in the tie-break as he advanced to the last four.