The duo tore Bolton to pieces with Agbonlahor twice on the mark to take his league haul to nine this season as Villa warmed up for their UEFA game in Hamburg on Wednesday.
The win, which was Villa's first home success since their victory over Blackburn on October 29, keeps them well on course as they moved back into the top four.
Villa Park is not one of Bolton's happy hunting grounds as they were beaten 4-0 in the corresponding game last season when they hit rock bottom.
With three former Villa players, Gary Cahill, Gavin McCann and JLloyd Samuel, in their side, Bolton operated a successful offside plan which caught out the opposition three times in the opening ten minutes, but in the end they had no answer to the threat of Agbonlahor and Young.
The early play was less than fluent from either side and it developed into a battle of wits but the fans later had full value for money with six goals in the game.
The stalemate was surprisingly broken in what was Bolton's first concentrated attack in the 17th minute when Kevin Davies somehow managed to swing over a low cross despite the close attention of Martin Laursen.
Johan Elmander instinctively proved why he is Bolton's leading goalscorer when he slipped a first time close- range shot goalwards. Brad Friedel managed to get his hand to the ball but could not prevent the goal.
Villa found themselves up against a Bolton side that could not be underestimated following their recent impressive wins over Sunderland, Manchester City, Hull City and Middlesbrough which had earned manager Gary Megson the manager of the month award.
Boosted by Elmander's goal Bolton very nearly increased their advantage when Gretar Steinsson's header cannoned against the crossbar.
Following this let-off Villa got back into the game with some a fine solo goal from Agbonlahor in the 25th minute.
Despite the close attention of Andy O'Brien the young Villa striker nudged on Laursen's long pass, ran on to the ball and glided his shot past Jussi Jaakelainen.
Matthew Taylor blasted a golden opportunity over the bar and yet again Villa prospered from the let-off when the luckless Davies, challenged by Laursen, headed into his own goal four minutes before the break.
Referee Lee Probert who had earlier ignored a bad tackle on Ashley Young by Steinsson blotted his copy-book on the stroke of half-time when he missed a blatant handling offence by Cahill in the penalty area from a corner.
In the second half the deceptive strong running of Ashley Young was an obvious danger.
Young had been slow to emerge but his subsequent brilliance opened up Bolton's defence for Villa's third goal after 67 minutes.
Agbonlahor, who has developed a very good understanding with Young, was on hand to net his second goal when he headed home a cross from the winger.
The pair joined forces again in the 78th minute and this time it was Agbonlahor who set up Young to score with an accurate low drive past the helpless Jaaskelainen.
Bolton grabbed a consolation goal four minutes from time when Davies headed in a right-wing cross from Steinsson.