Valtteri Bottas was top of the timesheets at Monza with a fastest lap of one minute 20.703 seconds on the soft tyres, with six times champion team mate and overall leader Hamilton 0.245 slower.
Verstappen, second overall and 47 points behind Hamilton after seven races, spun off across the gravel and into the barriers at the Ascari chicane and damaged his front wing.
The incident brought out the red flags but Verstappen, who returned to the pits, was able to get back on track later and ended up fifth.
"Thankfully it was just a front wing. We're not flush with parts so we'll need it back from the marshals a bit later," Red Bull team boss Christian Horner told Sky Sports television.
"It's very high speed over there, so we're lucky to get away with the low-ish amount of damage that we did."
The Dutch driver's Thai team mate Alexander Albon was third fastest, but 0.797 off Bottas's pace, with Russian Daniil Kvyat fourth for AlphaTauri.
Neither of the two Ferraris featured in the top 10 with their car short of straight-line speed at the fastest track of the year.
Monegasque Charles Leclerc, last year's winner, was only 11th with Sebastian Vettel down in 19th and behind Williams' Israeli test driver Roy Nissany, taking George Russell's seat for the session. (Reporting by Alan Baldwin in London, editing by Toby Davis)