Joleon Lescott scored the only goal of the game midway through the second half to consign the club he supported as a boy to a seventh home match without a league for the first time in 25 years.
Joe Hart had very little to do throughout the 90 minutes against a frustratingly unambitious Villa, but he made a vital save in the closing stages to ensure all three points for his team.
For Villa, their third league defeat in six games leaves them in the bottom six following West Bromwich Albion's emphatic 5-1 derby win over Wolverhampton Wanderers earlier on Sunday. There is a seven-point gap between them and the five clubs at the bottom of the table, but that is unlikely to spare Villa boss Alex McLeish coming under increased pressure.
City beat Villa 4-1 at the Etihad Stadium back in October, and when Sergio Aguero's swivel-and-shot after just three minutes flew right at Shay Given it looked as though Alex McLeish's side were in for another torrid afternoon.
However for all their dominance of possession - at one point hogging as much as 76 per cent of the play - the Citizens' recent troubles in scoring away from home continued. Before their arrival at Villa Park they had only scored once in their last four league games on the road.
Aguero's recent form reflects that of City. The Argentina striker's penalty against Fulham last weekend was his first in six games for city, and he hit another tame effort that Alan Hutton cleared as it trickled towards the net.
Villa defender Richard Dunne came as close as anyone on the home side to scoring against his former club with a header from a free-kick that was an easy catch for Joe Hart before sending a similar effort from a corner over the bar.
City continued to hog the possession and dominate the shot count after the break. Vincent Kompany's glanced header was nodded to safety by James Collins, Lescott headed over the bar from an excellent free-kick delivery and Silva and Pablo Zabaleta stung the palms of Given after he was teed up for a strike from range by Aguero.
They finally made the breakthrough on 63 minutes when Gareth Barry headed a corner back across goal and Lescott pounced to finish on the turn from close range. The goal was his second of the season and the fifth he has scored against Villa in his career.
McLeish eventually responded by bringing on Charles N'Zogbia for Emile Heskey, who had been playing almost as an auxiliary right-back at times. Soon afterwards he also brought on Stephen Ireland, whose introduction took the tally of players on the field to play for both clubs to five.
A belated fightback from the home side resulted in a header over the bar from Cuellar before Collins' persistence forced Aleksandar Kolarov into conceding another in injury time. From the set piece Darren Bent shot on the turn inside the six-yard box. Just as he did in City's last away win at Wigan, Hart reacted brilliantly to pull off a save which was a key to claiming victory as the single goal at the other end.
However, victory does not paper over the faults that have appeared in City's usually well-oiled machine since the departure of Yaya Toure for the African Cup of Nations. The midfielder and his brother Kolo will both be back in time for City's next game once their final appearance in that tournament with Ivory Coast is over.