Gomis put the French side ahead midway through the first half with a classy chip before Kone effectively sealed three points with a tap-in two minutes before the break.
It meant Lyon marked their 100th Champions League game with victory as they dominated their Croatian opponents to move three points clear in second behind Real Madrid.
Lyon should have taken an early lead when Gomis squandered a good chance in the third minute as he fired over from just six yards after the ball had broken loose in the box.
The French side were dominating the early proceedings, Jimmy Briand unable to direct his header on target from Michel Bastos' cross while Maxime Gonalons shot over the bar.
Lyon's pressure paid off midway through the half when Gomis opened the scoring with an impressive goal as he found himself one-on-one with Ivan Kelava and chipped the goalkeeper from 20 yards, the ball going into the top left-hand corner.
The hosts were overpowering the Croatians, Mateo Kovacic just poking the ball away for a corner after Anthony Reveillere had glided past him on the right wing.
Dinamo relieved the pressure as Luis Ibanez's free-kick hit the wall before team-mate Adrian Calello put a shot over the bar.
Ibanez put in a low ball from the left which Fatos Beqiraj just failed to reach as the visitors began to work their way into the game.
Both sides fired long-range shots over the bar before Gomis stabbed at the ball and sent it high when he could have doubled his side's lead.
However, his miss was cancelled out four minutes later when Bakary Kone put Lyon 2-0 up.
Clement Grenier whipped in a corner from the left and Kone found himself unmarked in front of goal, just side-footing the ball into the net.
Grenier was then denied by Kelava on the stroke of half-time as the French side cruised into the break.
Dinamo started the second half positively, Ibanez and Josip Simunic seeing shots blocked.
Ibanez then laid the ball off to Jorge Sammir whose shot from the edge of the box was comfortably caught by Hugo Lloris.
Lloris also punched clear from an Ibanez corner before the keeper made a crucial save, diving to keep out Tonel's goalbound header.
While Dinamo were enjoying more possession, the hosts were still threatening on the counter-attack, Briand halted as he ran towards goal while Bastos shot a free-kick over the bar.
Calello and Ibanez both had shots on goal for Dinamo while Lloris parried an attempt by Leko but time ran out for Dinamo as Lyon enjoyed a highly-deserved victory.