Vokes headed the hosts in front from a fine Bale cross after 38 minutes before Allen capitalised on a goalkeeping error to make it 2-0 six minutes later.
Ivan Jardan's ill-advised backpass then gifted Bale his first of the night after 50 minutes and the Real Madrid star added another from the penalty spot - his 24th international goal putting him four behind his country's all-time top scorer Ian Rush - deep into stoppage time.
Moldova, who came into the game 154 places below Wales in the FIFA rankings, never looked capable of avoiding defeat and barely mustered a meaningful attack over the course of the 90 minutes.
Chris Coleman's men, meanwhile, were a little slow out of the blocks, but effectively had the Group D game sewn up by half-time and could easily have won by an even more emphatic scoreline. The result extended Wales' unbeaten home run in competitive internationals that dates back to September 2013.
The opening quarter was decidedly light on goalmouth incident, although it was Wales who looked the more purposeful with Bale firing a long-range free-kick over and Joe Ledley drawing a regulation save from Ilie Cebanu with a low shot.
Wales continued to dominate possession as the half wore on and eventually found a way through Moldova's dogged defence seven minutes before the interval.
Bale provided the inswinging cross from the right and Vokes planted a firm, downward header past Cebanu.
And the home side then doubled their advantage just before the break as Allen swept home the loose ball after Cebanu's weak attempt to punch away a Ledley corner.
That reprieve proved a very temporary one for Moldova as five minutes into the second half, Bale did grab his side's third.
Jardan's backpass turned into a throughball for Bale and he raced clear to calmly find the bottom corner of the net.
Bale then had the final say in the 95th minute after he was bundled over in the box by Adrian Cascaval, stepping up to fire home from the spot.