Crutchlow even had a qualifying tyre left in his pit box as he had completed the first two Superpole sessions using race tyres, having spent most of practice riding on worn tyres to find a strong set-up for raceday.
Aprilia Alitalia rider Max Biaggi went second quickest on his vee-four machine in a session when the top five riders were competing with five different makes of machinery - Yamaha, Aprilia, Ducati, Suzuki and Honda.
With both factory Ducati Xerox machines ruled out early from the reckoning, after a Superpole 1 crash for Michel Fabrizio and a tough Superpole 1 session in general for Noriyuki Haga, Carlos Checa was once more best Ducati rider, taking his private Althea machine to third-best grid placing.
Leon Haslam (Suzuki Alstare) could not make the most of his qualifying tyres and was fourth on the grid, but still starts from the front row for Sunday's 22-lap races.
Jonathan Rea (Hannspree Ten Kate Honda) was a battling fifth, ahead of Pata B&G Ducati rider Jakub Smrz, and Checa's fast team-mate Shane Byrne. The last place on the second row went to Troy Corser, who recovered from a technical problem in Superpole 1 to finish eighth overall. Top Kawasaki starting slot belongs to Tom Sykes (Kawasaki Racing Team) after he was 12th in Superpole.
James Toseland (Sterilgarda Yamaha) crashed in Superpole two, and Max Neukirchner also had a fast fall, destroying his number one bike. He finished 13th, Toseland 15th.
Chris Vermeulen (Kawasaki Racing Team) will not race at Portimao, still suffering effects from his Phillip Island crash.
Cal Crutchlow: "We made some changes since the last race. Yamaha has worked really hard in the last month to work out our problems as well. The track here is better and better and our bike is also improving. I was quietly confident I could get pole and we even had one qualifying tyre left at the end because we used race tyres in the first two sessions. Pole is a bonus."
Max Biaggi: "We made a good race here last year so we know what our level would be. Now we are back where we should be, fighting with the best guys on the top. We did not make many changes just got the set-up to work as best we can. The layout of the track and the tarmac just means that our bike is working better."
Carlos Checa: "I think it is open tomorrow, because many riders have good pace with a chance to win and be at the front. We will see how the race turns out, but hopefully we will be there at the end and have a chance."
Times: 1. Crutchlow C. (GBR) Yamaha YZF R1 1'42.092; 2. Biaggi M. (ITA) Aprilia RSV4 1000 F. 1'42.513; 3. Checa C. (ESP) Ducati 1098 R 1'42.586; 4. Haslam L. (GBR) Suzuki GSX-R1000 1'42.596; 5. Rea J. (GBR) Honda CBR1000RR 1'42.807; 6. Smrz J. (CZE) Ducati 1098R 1'42.8897. Byrne S. (GBR) Ducati 1098R 1'42.960; 8. Corser T. (AUS) BMW S1000 RR 1'43.152; 9. Guintoli S. (FRA) Suzuki GSX-R1000 1'42.984; 10. Xaus R. (ESP) BMW S1000 RR 1'42.999; 11. Camier L. (GBR) Aprilia RSV4 1000 F. 1'43.039; 12. Sykes T. (GBR) Kawasaki ZX 10R 1'43.199; 13. Neukirchner M. (GER) Honda CBR1000RR 1'43.380; 14. Lanzi L. (ITA) Ducati 1098R 1'43.568; 15. Toseland J. (GBR) Yamaha YZF R11'49.401; 16. Scassa L. (ITA) Ducati 1098R 1'44.249
Supersport World Championship - Laverty on pole at his team's home track
Eugene Laverty (Parkalgar Honda) pushed his way to the pole time at Portimao, with Hannspree Ten Kate Honda riders Kenan Sofuoglu and Michele Pirro second and third. Top Kawasaki rider was Joan Lascorz in fourth, with the best Triumph BE1 machine under the control of Chaz Davies, sixth on the timesheets. Local rider Miguel Praia (Parkalgar Honda) was eighth and now starts from the second row.
Times: 1. Laverty E. (IRL) Honda CBR600RR 1'45.169; 2. Sofuoglu K. (TUR) Honda CBR600RR 1'45.313; 3. Pirro M. (ITA) Honda CBR600RR 1'45.828; 4. Lascorz J. (ESP) Kawasaki ZX-6R 1'45.903; 5. Foret F. (FRA) Kawasaki ZX-6R 1'46.082; 6. Davies C. (GBR) Triumph Daytona 675 1'46.161; 7. Fujiwara K. (JPN) Kawasaki ZX-6R 1'46.415; 8. Praia M. (POR) Honda CBR600RR 1'46.566
Superstock 1000 FIM Cup
Ayrton Badovini (BMW Motorrad Italia) will start Sunday's race from pole position, having held off the push of Maxime Berger (Ten Kate Race Junior) in combined qualifying. Marco Bussolotti (All Service System Honda) went third and Eddie La Marra (Team Lorini Honda) was fourth, each having moved up from Superstock 600 racing this year.
Times: 1. Badovini A. (ITA) BMW S1000 RR 1'45.773; 2. Berger M. (FRA) Honda CBR1000RR 1'46.241; 3. Bussolotti M. (ITA) Honda CBR1000RR 1'46.609; 4. La Marra E. (ITA) Honda CBR1000RR 1'46.759; 5. Baz L. (FRA) Yamaha YZF R1 1'46.821; 6. Magnoni M. (ITA) Honda CBR1000RR 1'46.839; 7. Antonelli A. (ITA) Honda CBR1000RR 1'46.884; 8. Baroni L. (ITA) Ducati 1098R 1'46.895
Superstock 600 Race - 10 Laps
In the first race of the season for the Superstock 600 riders pole man Florian Marino (Ten Kate Junior Honda) was a first lap faller, leaving Jeremy Guarnoni (MRS Racing Yamaha) a clear run to the win. Second was Romain Lanusse (MRS Racing Yamaha) and third Frederik Karlsen (MTM Racing Yamaha).
Times: 1. Guarnoni J. (FRA) Yamaha YZF R6 18'18.901 (150,434 kph); 2. Lanusse R. (FRA) Yamaha YZF R6 6.101; 3. Karlsen F. (NOR) Yamaha YZF R6 6.277; 4. Calero Perez N. (ESP) Yamaha YZF R6 6.527; 5. Fanelli D. (ITA) Honda CBR600RR 7.916; 6. Cecchini R. (ITA) Triumph Daytona 675 10.090; 7. Lombardi B. (ITA) Yamaha YZF R6 10.724; 8. Major N. (FRA) Yamaha YZF R6 14.105