The Kawasaki rider fell outside the top 10 in FP3 and was forced into SP1 for the first time since the current qualifying format came into effect.
However, the Briton soon put his earlier woes behind him and broke the lap record in the first afternoon session with a time of 1m 34.4s.
Sykes then bettered that time early on in SP2 with a final time of 1m 32.214s, which was more than half a second faster than his pole-setting time of 2014.
As a result, Sykes has become the first rider to claim pole position in the history of the Championship having come through SP1 earlier.
The front row is completed by Leon Haslam and Davide Giugliano, who would both be quite satisfied with a front row berth.
Haslam had been the fastest of the riders in the early parts of SP2 and was particularly quick on one-lap stints, but wasn’t as comfortable as Sykes on the softer rear Pirellis to finish two tenths behind the pole-sitter
Giugliano has had a troubled weekend in front of his home fans after crashing during FP1 and was only sixth fastest on his first hot lap in SP2. In his next attempt, the Italian matched Haslam’s best, finishing just a hundredth of a second behind the Aprilia rider,
World Championship leader Jonathan Rea had to settle for fourth place and looked like he might get a front row berth, but had no answer to Sykes’ pace, leaving him on the second row just ahead of the returning Max Biaggi.
Biaggi, participating in his first Superbikes race in more than two years, was within a tenth of Sykes’ time but was unable to maintain that early momentum to finish just behind the Kawasaki man.
Catalan Jordi Torres had led proceedings early on but dropped down to the last spot on the second row, ahead of Crescent Suzuki's Alex Lowes, Ayrton Badovini and Sylvain Guintoli
The top 10 was rounded out by Ducati stand in rider Michele Pirro,with Chaz Davies in a disappointing 11th.
Pirro stands in for the injured Luca Scassa and made his first appearance earlier on Saturday morning.
Full Superpole qualifying results from Misano:
1. Tom Sykes GBR Kawasaki Racing ZX-10R 1m 34.214a
2. Leon Haslam GBR Red Devils Roma Aprilia RSV4 1m 34.426
3. Davide Giugliano ITA Aruba.it Racing Ducati 1199R 1m 34.442
4. Jonathan Rea GBR Kawasaki Racing ZX-10R 1m 34.459
5. Max Biaggi ITA Red Devils Roma Aprilia RSV4 1m 34.463
6. Jordi Torres ESP Red Devils Roma Aprilia RSV4 1m 34.551
7. Alex Lowes GBR Voltcom Crescent Suzuki GSX-R1000 1m 34.811
8. Ayrton Badovini ITA BMW Italia S1000RR 1m 34.881
9. Sylvain Guintoli FRA PATA Honda CBR1000RR 1m 35.061
10. Michele Pirro ITA Aruba.it Racing Ducati 1199R 1m 35.139
11. Chaz Davies GBR Aruba.it Racing Ducati 1199R 1m 35.473
12. Matteo Baiocco ITA Althea Ducati 1199R 1m 35.862
Grid positions determined by SP1
13. Leandro Mercado ARG Barni Ducati 1199R 1m 35.285
14. Niccolò Canepa ITA Althea Ducati 1199R 1m 35.464
15. Michael van der Mark NED PATA Honda CBR1000RR 1m 35.642
16. Markus Reiterberger GER BMW S1000 RR 1m 35.658
17. Roman Ramos ESP GO Eleven Kawasaki ZX-10R1m 36.205
18. Leon Camier GBR MV Agusta F4 RR 1m 36.247
19. Randy de Puniet FRA Voltcom Crescent Suzuki GSX-R1000 1m 36.262
20. David Salom ESP Pedercini Kawasaki ZX-10R Did not set time
Did progress to Superpole, grid positions determined
21. Santiago Barragan ESP Grillini Kawasaki ZX-10R 1m 38.523
22. Gianluca Vizziello ITA Grillini Kawasaki ZX-10R 1m 38.675
23. Christophe Ponsson FRA Pedercini Kawasaki ZX-10R 1m 38.931
24. Gabor Rizmayer HUN Team Toth BMW S1000RR 1m 39.792
25. Imre Toth HUN Team Toth BMW S1000RR 1m 41.415s