Both Classic TT and Manx Grand Prix riders recorded timed laps after mist around the course caused a delay.
Anstey's lap of 121.932mph was the quickest followed by Ivan Lintin (121.094), Derek Shiels (121.04) and Horst Saiger (120.89).
Michael Dunlop was reported as an early retirement at Ballacraine.
Clerk of the course Gary Thompson told all competitors before the session of a number of damp patches around the course.
Classic TT riders Grant Dalton, Elwyn Fryer and Dean Osborne all came off but were reported as fine.
Local racer Michael Evans topped the Manx Grand Prix qualifying board on his Senior Martin Bullock Motorsport Suzuki with 116.347.
Tom Robinson, from Barwick, was hot on his heels posting a lap of 116.135 to top the Junior timesheets from Australian Royce Rowe (115.203).
The MGP newcomers recorded their first timed laps after Saturday's untimed session, with the top 10 all averaging more than 100mph.
Manchester's Mike Norbury led the way at 109.138mph.
Meanwhile, Nick Anderson was taken to Noble's Hospital with a shoulder injury and Matt Stevenson came off at Governors.
The third qualifying session will be held on Wednesday.
New Zealand's multiple TT winner Bruce Anstey set the pace in a weather-delayed second practice session for the 2017 Festival of Motorcycling.