Jose Mourinho's United are also second. But they are two points behind Group H leaders Juventus whom they host on 23 October at Old Trafford.
United's stalemate came three days after they lost 3-1 at West Ham United. That display and Tuesday night's setback prompted a barrage of criticism most notably from the former United midfielder Paul Scholes who claimed Mourinho is embarrassing the club with repeated outbursts at his players in the media.
Mourinho responded: "Freedom of speech, free country, you can say what you like. Freedom of speech, especially for Man Utd fans that I respect 100 percent."
In an effort to ignite his strike force, Mourinho recalled Alexis Sanchez to the starting line-up. But the Chilean was unable to sparkle and was substituted after 75 minutes.
"We knew we wouldn't create 20 chances," said Mourinho. "Our attacking players aren't in their best moments of confidence and individual level. We thought with three or four chances we would score and win the game."
Manchester City claimed the three points thanks to David Silva's strike in the 87th minute.
Hoffenheim stunned the visitors to the Wirsol Rhein-Neckar-Arena with a goal in the first minute. But Ishak Belfodil's opener was cancelled out soon after by Sergio Aguero.
After the victory, Guardiola hailed his team's fighting spirit. "Losing at home to Lyon made things tough and conceding so early at Hoffenheim was hard," said the Spaniard. "But we have to live this kind of situation.
"The previous two seasons weren't easy to qualify for the knockout stages but we still went through with one or two games left. I think it will come down to our final game this time."