Ligue 1 leaders Lyon, playing in Europe's elite club competition for the 12th consecutive time, were simply too good for Dinamo and goals from Gomis and Kone made sure they remained two points behind group leaders Real Madrid.
"We had pretty much done what was needed at half-time. Hats off to the players, I am proud of them," coach Remi Garde told the French TV channel TF1.
"It is going according to plan. Zagreb could not play their game because we defended very well and since we were strong offensively it was all good."
Lyon, who did not bring in any major signings during the close-season, have been relying on youngsters and the policy is paying off.
Kone, who joined from Ligue 2 side Guingamp, has been impressive in central defence this season.
The 20-year-old Clement Grenier, groomed at Lyon's youth academy, has also been in sparkling form in midfield, showing he has what it takes to make up for Bosnian Miralem Pjanic's move to AS Roma.
Lyon made a good start at a packed Gerland stadium and Gomis skied a third-minute effort over the bar in front of a gaping net.
Maxime Gonalons also missed a clear chance in front of goal but Lyon's domination was eventually rewarded.
In the 23rd minute Gomis, who missed a string of opportunities in the game, delicately chipped the ball over keeper Ivan Kelava to put the hosts ahead.
It was Gomis's seventh goal from 10 games in all competitions this season and the former St Etienne striker looks likely to be recalled by France coach Laurent Blanc on Thursday for two important Euro 2012 qualifiers.
The unmarked Kone added a second goal before Grenier almost notched a third on the stroke of half-time, Kelava diving at his feet to deny the French midfielder.
Lyon keeper Hugo Lloris pulled off a superb save in the 71st minute, diving to his right to palm away a Tonel header for Dinamo.
Lloris made another excellent stop to his left six minutes from time after a low shot by Jerko Leko.
Lyon, who have never won the Champions League but reached the semi-finals in 2009-10, next face Real Madrid in three weeks' time at the Santiago Bernabeu.
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