After finishing the day's first session almost half a second ahead of his rivals, the Roman – who had retired from racing at the end of the 2012 season – had to work much harder to top the standings in the second session.
Giugliano missed most of the first after crashing early on but made a tremendous recovery and seemed destined to time the standings before Biaggi beat his time by a quarter of a second with the chequered flag about to be raised.
In fact, Biaggi's time was two tenths faster than the official lap record held by Tom Sykes.
Before Biaggi's late rally going into the final 10 minutes of the session, the top five was separated by just a tenth of a second.
Behind the 25-year-old Giugliano was his Ducati team-mate Chaz Davies, whose best time was just six thousandths of a second slower than the Italian's.
Leon Haslam on the sister Aprilia was in fourth place another tenth behind, while the Kawaski pair of Jonathan Rea and Sykes were split by just five hundredths.
In fact, Sykes' best time was just a tenth off second place.
Jordi Torres on the third Aprilia on the grid was a seventh, two tenths further behind, while Leandro Mercado on the Ducati finished in eighth.
Suzuki rider Alex Lowes finished in the top 10 for the second time on the day with a credible ninth, while Matteo Baiocco on the Ducati rounded out the top 10.
Englishman Leon Camier suffered with various mechanical problems in the first session, but managed to put his Agusta F4 in 15th place in the afternoon session, despite finishing just 13 laps.
While Giugliano responded well following his crash early in the day, Dutchman Michael van der Mark struggled after his spill earlier and could only finish 17th in FP2.
After finishing FP1 in fourth place, German wildcard Markus Reiterberger dropped down to 12th in the afternoon.
Halfway through the session proceedings came to a halt when Christophe Ponsson fell from his Pedercini Kawasaki. The Frenchman was taken to the medical centre for treatment and the early reports suggest that he came through the incident unscathed.
Collated Second Practice session times:
1. Max Biaggi ITA Red Devils Roma Aprilia RSV4 1m 35.380s
2. Davide Giugliano ITA Aruba.it Racing Ducati 1199R 1m 35.631s
3. Chaz Davies GBR Aruba.it Racing Ducati 1199R 1m 35.637s
4. Leon Haslam GBR Red Devils Roma Aprilia RSV4 1m 35.652s
5. Jonathan Rea GBR Kawasaki Racing ZX-10R 1m 35.672s
6. Tom Sykes GBR Kawasaki Racing ZX-10R 1m 35.735s
7. Jordi Torres ESP Red Devils Roma Aprilia RSV4 1m 35.966s
8. Leandro Mercado ARG Barni Ducati 1199R 1m 36.015s
9. Alex Lowes GBR Voltcom Crescent Suzuki GSX-R1000 1m 36.052s
10. Matteo Baiocco ITA Althea Ducati 1199R 1m 36.096s
11. Sylvain Guintoli FRA PATA Honda CBR1000RR 1m 36.116s
12. Markus Reiterberger GER BMW S1000 RR 1m 36.186s
13. Ayrton Badovini ITA BMW Italia S1000RR 1m 36.510s
14. David Salom ESP Pedercini Kawasaki ZX-10R 1m 36.557s
15. Leon Camier GBR MV Agusta F4 RR 1m 36.657s
16. Niccolò Canepa ITA Althea Ducati 1199R 1m 36.796s
17. Michael van der Mark NED PATA Honda CBR1000RR 1m 36.841s
18. Randy de Puniet FRA Voltcom Crescent Suzuki GSX-R1000 1m 36.935s
19. Roman Ramos ESP GO Eleven Kawasaki ZX-10R1m 37.230s
20. Luca Scassa ITA Aruba.it Racing Ducati 1199R 1m 37.243s
21. Gianluca Vizziello ITA Grillini Kawasaki ZX-10R 1m 38.772s
22. Christophe Ponsson FRA Pedercini Kawasaki ZX-10R 1m 38.931s
23. Santiago Barragan ESP Grillini Kawasaki ZX-10R 1m 39.493s
24. Gabor Rizmayer HUN Team Toth BMW S1000RR 1m 40.832s
25. Imre Toth HUN Team Toth BMW S1000RR 1m 43.190s