Dynamo are on four points in Group F alongside Barcelona and Rubin Kazan following Barca's shock defeat by the Russians while Inter, who have flattered to deceive in the Champions League for years, are bottom after three draws in their first three games.
Enterprising Dynamo took the lead after five minutes when Taras Mikhalik was given time to rifle in off the post following poor defending from the Italian champions.
With Inter struggling to mount an attack, Dynamo's former AC Milan striker Andriy Shevchenko almost grabbed the headlines on his return to a half-empty San Siro when his header whistled just wide.
Dejan Stankovic brought Jose Mourinho's side level on 35 minutes when he was played through by Lucio and knocked the ball past the onrushing goalkeeper from the edge of the area.
Parity did not last long, however, with Lucio heading a corner into his own net under pressure.
ANOTHER CORNER
"I didn't expect to have just three points after the first three games but in soccer the difference between winning and drawing is very little," Mourinho told a news conference.
"This is a group with great difficulties. It's a group with four champions. I think we'll go through, it's my conviction."
Samuel Eto'o, back after a foot problem, took Balotelli's place as the lone striker but apart from a penalty appeal and one good chance he barely troubled the visiting defence.
"No one is disappointed, we are totally satisfied with what we have done from the start to the finish. Tonight's formula worked well," said Dynamo coach Valeri Gazzaev, whose side host Inter next on November 4.
