Fresh from losing to Cardiff City last weekend, the 2012 Premier League champions were again given a fright against a promoted club before eventually claiming a second win of the season.
In a lively start, Hull should have taken the lead after seven minutes when Sone Aluko burst clean through, but he scuffed his shot wide when he could have rounded Joe Hart.
The Tigers then had the ball in the net four minutes later, but Danny Graham's clinical first-time finish from Robbie Brady's delicious cross was rightly ruled out for offside.
The hosts responded with Joleon Lescott's header forcing a reaction stop from Allan McGregor before Robert Koren's volley whistled just wide at the opposite end.
Manuel Pellegrini brought on Negredo for Edin Dzeko at half-time and the decision was rewarded on 65 minutes when the summer signing headed home Pablo Zabaleta's deep cross.
Hull refused to give up, but the game was put beyond their reach in the final minute when Toure curled a sumptuous free-kick over the wall and in off the underside of the bar.
The home side were slow out of the blocks and Hull took advantage of their lethargy, frustrating their opponents with their determination to defend strongly and chase everything.
Hart, under scrutiny for club and country after an indifferent start to the season, seemed uncertain as Hull made an early move into the box but Zabaleta cleared the danger.
Graham's pass on seven minutes took a fortunate ricochet off Matija Nastasic and sent Aluko clear, but he squandered the glorious opportunity after reaching the edge of the area unchallenged.
It sparked a lively passage of play and the in-form McGregor saved superbly at his near post from a Dzeko header at a corner.
On-loan Sunderland striker Graham was then marginally offside when connecting with Brady's ball into the box, while McGregor was in action again moments later, tipping over a powerful Lescott header from a delicate David Silva cross.
Manchester City were unable to impose themselves and frustration among the fans was evident, even as early as the 30-minute mark.
Sergio Aguero weaved his way through the Hull defence with a typical jinking run but then lifted the ball into McGregor's arms.
Pellegrini attempted to inject his side with fresh life at the start of the second half, sending on summer signing Negredo in place of Dzeko.
Yet it took Negredo some time to find his radar, with his first contribution being to head a long way wide from a Silva cross three minutes after coming on.
They finally produced some quality to break the deadlock with a good attack down the right in the 65th minute.
Zabaleta got behind the defence and whipped in an inviting cross for Negredo, who moved into space and leapt high to plant a firm header past McGregor.
The goal appeared to do the job for the home side and they then played out until the final whistle. They sat back and looked to strike on the break but they were again unable to muster much to worry Hull.
The visitors pressed until the end and they tried to have one last crack, but Hart punched a Tom Huddlestone free-kick away convincingly and then cleared an Ahmed Elmohamady cross.
And the points were safe in the final minute when substitute Samir Nasri was fouled on the edge of the box and Toure stepped up to curl in a superb free-kick, despite Elmohamady tracking back to the goal-line.