The Holland international has not played a first-team game since dislocating his ankle in an Intertoto Cup clash with BK Odense in July 2008.
Left-back Bouma's initial comeback stalled in March after three reserve games when suffering a reaction to the ankle setback.
Hoping to return: Villa's Bouma in action against Portsmouth in December 2007
Then in October he played one reserve game only to sustain a toe problem.
Now he has completed another 90 minutes for the reserves - against Chelsea at Villa Park on Monday night - and is keeping his fingers crossed his troubles are behind him.
Villa boss: O'Neill
Bouma said: 'I'm very pleased because it was my first game back after a long time out.
'I've only been back in training for 10 days so I was delighted with what I could do last night.
'Before the game we had said if I could get an hour it would be great and anything more would be even better, so to play the whole 90 minutes I'm very pleased.
'I felt great. I've been here before but it's always great to be back out on the pitch.
'You have to get back to full match fitness and just take it a little bit easy.
'But you can't really take it easy because sometimes you will need to go in as hard as you can on the pitch. That's exactly what I did and thankfully I came out of it okay.'
Bouma added: 'I'm really, really happy. This is now the third time on the comeback trail so hopefully it's third time lucky and I've got everything bad out of the way and behind me.'
Martin O'Neill's Villa are enjoying a fine season again, with Saturday's 2-0 win at Fulham keeping up their hopes of a fourth placed finish.
And they face Manchester United in the Carling Cup final at Wembley later this month.
Shorey joins Fulham on loan with view to permanent switch from Aston Villa Martin O'Neill plays down Villa's Champions League hopes despite thumping win at FulhamASTON VILLA FC