He added in media interviews: "It has been quite a smooth day. We're not as fast as the Red Bulls, but we are still confident.
"The Red Bull is quick but generally the car feels good so I have to sit and try and understand [where to find the pace].
"I feel like I am on the limit everywhere and the car feels reasonably balanced.
Italian GP: Practice one highlights - Hamilton fastest
But Hamilton said he did not feel particularly optimistic that he could take pole on Saturday, for what would be the fifth consecutive race.
"Right now, it doesn't look massively strong for tomorrow," he said. "But hopefully we can improve the pace."
Alonso was fifth fastest in second practice, 0.877secs slower than Vettel.
The Spaniard has admitted he must try to finish in front of Vettel this weekend to prevent the German extending his lead any further than the current 46 points.
Ferrari team principal Stefano Domenicali admitted Red Bull "seem very strong", adding: "We have two races in front of us [in Italy and then Singapore] where if we are not able to deliver a good result it will be very difficult to stay connected to the leader, so for sure it is very crucial."
The times set on the race-simulation runs, on which teams run race levels of fuel, were more encouraging for Ferrari.
Webber's average over a 16-lap run on medium tyres, on which he appeared to be simulating the first stint of the race was one minute 29.129 seconds, while Alonso's on a similar 14-lap run was 1:29.293.
Hamilton did 1:29.461 and Raikkonen 1:29.544, while Rosberg averaged 1:29.149 on the hard tyre.
Vettel did not do a comparable run - he ran on the hard tyre when Webber and Alonso were on the mediums.
The teams do not reveal the fuel loads they were using at the time, so it is impossible to make an accurate comparison.
Italian Grand Prix, day two
Saturday, 7 September : Final practice at 09:55 BST on BBC Two, Radio 5 live sports extra, plus live text commentary online. Qualifying at 12:10 BST on BBC One, Red Button, Radio 5 live plus live text commentary online
Italian Grand Prix, day three
Sunday, 8 September: Race coverage at 12:10 BST on BBC One & BBC Red Button at 13:00 BST, plus Radio 5 live at 13:00 BST, and live text commentary online. F1 Forum, 15:15 BBC Red Button. Highlights, 19:00 BBC Three & BBC Red Button
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