Hamilton said in Bahrain on Thursday that Mercedes' understands Ferrari has eliminated its power deficit this season.
Having topped FP2 as Ferrari enjoyed a comfortable advantage on Friday, Raikkonen remained fastest in FP3 and his laptime of 1m29.868s left him a full 0.525s ahead of the Red Bull pair of Max Verstappen and Daniel Ricciardo.
The Australian was also blocked on his fastest lap - by Bottas.
The British star had wound up fourth fastest earlier in Friday's second free practice session at the Bahrain International Circuit. That would have meant his tyres were not at their absolute optimum when Hamilton did his next lap.
Eight minutes later, the session resumed.
Raikkonen, however, faced a post-race investigation into a possible "unsafe release" of his vehicle, by Ferrari, following a routine pit-stop late in the session.
Even Red Bull's pace was not necessarily their optimum. Daniel Ricciardo (Red Bull) +0.440s 6.
"We're focusing on our selves, on the set-up mostly and try to get a better feel which at times was good, other times was not yet there". But that came courtesy the timely deployment of the virtual safety auto with Hamilton, until then, set to wrap up a comfortable victory in his Mercedes which had a clear edge over Vettel's Ferrari all weekend.
Vettel will want the honours to continue coming in, and while he won last week, the Ferrari star will be wary of a Mercedes team that will want to storm back.
"For now I'm chuffed and for the team as well as we had some issues this morning and we overcame them", said the German. "They've been a bit better with their tyres, they always are in hot places like this".
"We need to wait", said Vettel. "I didn't know it was in but I thought I had the delta". It looked like we were a bit quicker than the rest but it depends a bit on the programme.
In a sign of Mercedes' struggles, Bottas in sixth was closer to the two Renaults of Nico Hulkenberg and Carlos Sainz behind him than he was to the top three, with all the cars down to Sergio Perez in 14th place also with 0.6s of the Finn.
"Every year is different, every vehicle is different, it's a new auto and it's been pretty OK".
If Gasly and Alonso's positions are repeated on Saturday in qualifying, it would be embarrassing for McLaren at the home race for their chief shareholders, the Bahraini sovereign investment fund.
"It would be great to have a good result in Bahrain after such big disappointment in Australia", Magnussen said. He had been running on the supersofts but came in for a set of softs when the incident happened.