Fast bowler Lasith Malinga took two wickets off successive balls as England, electing to take first strike in good batting conditions, slumped from 168-1 to 258-5 by close of the opening day's play.
Vaughan hit 87 and opening partner Alastair Cook made 81 to give the tourists an early boost after they lost the first Test in Kandy.
But three unfortunate dismissals set England back by the end of an eventful day's cricket.
Vaughan said television replays should have been called for after frontline batsman Kevin Pietersen was given out caught in controversial circumstances in the post-tea period.
Pietersen edged Chaminda Vaas to second slip where Chamara Silva dived to scoop the ball off the turf and Kumar Sangakkara at first slip caught the rebound.
Australian umpire Daryl Harper consulted with his square-leg colleague Aleem Dar before ruling the batsman out without seeking the help of replays, which showed the ball hit the ground before Silva scooped it up.
Pietersen, who saw