The Serbian defender - who was booked for clearly catching the Villa striker's face in challenging for the ball - headed home Frank Lampard's free-kick on 73 minutes to give Jose Mourinho a second straight league win after Sunday's 2-0 success against Hull City Tigers.
John Terry was also fortunate not to avoid conceding a penalty in injury time when the ball clearly came off his hand from a Gabriel Agbonlahor header, but referee Kevin Friend decided to wave play on infuriating the Villa manager Paul Lambert and his players.
Mourinho's side were made to work for their three points against a robust Villa, who had opened their campaign with a 3-1 win at Arsenal on Saturday.
Chelsea moved ahead when Eden Hazard's shot was stopped by Brad Guzan only to come off the unfortunate Antonio Luna to nestle in the visiting net on six minutes.
Villa equalised in stoppage time in the first half when Benteke swept home Agbonlahor's cutback for his third goal of the season via a post, but they were destined to end the night in defeat by a referee who was not their friend.
PRE-MATCH: MATA AND TORRES IN Chelsea made two changes from their win over Hull City as Juan Mata and Demba Ba were brought in for Kevin de Bruyne and Fernando Torres. Defenders David Luiz and Tomas Kalas were Chelsea's other absentees. Brazil centre-back Luiz has a hamstring problem, but could return for Monday's trip to Manchester United, while Kalas suffered a fractured leg in pre-season.
BAKER OUT FOR VISITORS Aston Villa defender Nathan Baker missed out due to an ankle injury. The centre-back was forced off during Villa's 3-1 win at Arsenal on Saturday and was replaced by Ciaran Clark, who starts. Other than that Villa were unchanged. Manager Paul Lambert welcomed back key midfielder Yacouba Sylla, who missed the Emirates trip due to a twisted ankle but he is on the bench. Midfielder Chris Herd (calf) was still not quite ready to return to action.
8' OWN GOAL! Brad Guzan saves from Eden Hazard, but the ball comes back off Antonio Luna before nestling in the net. Chelsea ahead early on. Just like at the weekend against Hull.
44' INJURY PROBLEMS: A head gash for Clark and he requires some medical treatment. Clark departs the scene and is replaced by Jores Okore.
45+3' GOAL! Christian Benteke fires the ball low and hard into the net. No chance for Cech. Lovely run and cutback by Agbonlahor, who managed to evade Ivanovic. Ball in off the post. Villa level at 1-1.
64' VILLA CHANCE Fine stop by Cech! Benteke picks out Andreas Weimann on the run with a classy pass, but his shot is turned past a post by the Chelsea goalkeeper.
71' IVANOVIC FORTUNATE TO AVOID RED A booking for Ivanovic after he seemed to catch Benteke with an elbow in the air. Dangerous play by the Chelsea man, who escapes a red
73' GOAL! Ivanovic rises to head into the net from Lampard's free-kick. Brilliant free-kick and the header went beyond Guzan before he knew anything about it.
85' CECH RESCUES CHELSEA Brilliant stop by Cech as Weimann's effort on the half volley is stopped by the Chelsea goalkeeper. Excellent play by Benteke to play provider with the headed flick on.
90+2' TERRY HANDLES BUT NO PENALTY Huge Villa appeals for a handball against Terry in the Chelsea box. Seemed to catch the ball with his hand from Agbonlahor's header, but referee said no. Poor call by referee Kevin Friend.
TALKING POINT: How are Chelsea looking ahead of their trip to Manchester United on Monday? This is the type of match that the home side have to win if they are to mount a challenge for the title. Was not the most fluent of performances, but Chelsea stuck at it and earned their rewards. Also benefited from a couple of key decisions, or non decisions, by the referee Kevin Friend. The match at Old Trafford should be fascinating.
Chelsea: Cech 7, Ivanovic 7, Cahill 6, Terry 7, Cole 6, Ramires 6, Lampard 7, Oscar 6, Mata 5, Hazard 6, Ba 4..subs: Van Ginkel 6, Schurrle 6, Lukaku 6
Aston Villa: Guzan 7; Lowton 7, Vlaar 7, Clark 7, Luna 7; El Ahmadi 6, Westwood 7, Delph 7; Agbonlahor 7, Benteke 8, Weimann 7..subs: Okore 7, Tonev 6
Christian Benteke scores his 11th goal in 11 Premier League matches. He is top Premier League scorer this season with three goals and has scored more Premier League goals in 2013 (17) than any other player. Robin Van Persie is next on 14 goals.
Jores Okore comes on for Villa. He is the second OUTFIELD Danish player to play for the club after Martin Laursen. Goalkeepers Thomas Sorensen and Peter Schmeichel also played for Villa in the Premier League.
Villa extend their club record run to 24 Premier League matches without a clean sheet. Not since the 0-0 home draw with Stoke City on 8th December 2012 have they stopped the opposition scoring.
Branislav Ivanovic scores his fourth goal in four Premier League matches against Villa. He is second in the list of top Serbian Premier League scorers, one goal behind Nemanja Vidic (15).
Paul Lambert is still winless as a manager in the Premier League against Chelsea (one draw, four defeats). He has three wins from 13 Premier League matches in London (two draws, eight defeats).
Chelsea have won their opening two PL matches for the ninth time in the last 11 seasons (not 2006/07 or 2011/12). Villa have still not won their opening two Premier League matches since season 1999/2000.
MAN OF THE MATCH
Christian Benteke (Aston Villa) - Another superb forward performance from the Belgian striker, who was so unfortunate to be on the losing side. A third goal in two games for a man in form.
THE MATCH IN A TWEET