Hamilton lost just under five seconds behind his team-mate while the team vacillated over ordering Bottas to let the three-time world champion past.
Ferrari president Sergio Marchionne said he and his team now feel "completely confident" of mounting a championship challenge following Sebastian Vettel's victory in Sunday's Bahrain Grand Prix.
After the race, Hamilton apologised to the team for the incident and in his post-race media debrief revealed his frustration at the way the Bahrain weekend unfolded.
Past year was the first, and to date only, no-start of Vettel's Formula One career, with the vehicle breaking down on the formation lap at the desert circuit, but Sunday proved an evening to savour.
"Valtteri's problem was pretty clear, he was struggling in the first stint and that was clear, and afterwards you just need to have the tyres in the right window and obviously with Valtteri's auto we weren't able to have that".
But despite Bottas moving aside for a second time, a charging Hamilton ran out of laps to catch his championship rival.
Heading into this race, Vettel and Hamilton were level with a win each, but the latter's second victory of the season and 44th of his career puts him in command.
"It was a really great day", Vettel said. "Which I think is what racing should be about". It was a good start - our pace was key today to win.
Force India F1 boss arrested in United Kingdom over fraud allegations
Jaitley broached the matter with the UK's Chancellor of the Exchequer Philip Hammond and May when he visited London in February. The bank demands that he pay back more than a billion dollars in loans extended to his now-defunct Kingfisher Airlines.
Having started the Bahrain GP in pole position, Mercedes' Valtteri Bottas was feeling disappointed after ending up in third place.
"The pit lane was really my fault so apologies to my team for losing time there", Hamilton said.
"I was expecting a lot more personally".
"It's important as we start the race to give them equal opportunity", he said.
Bottas was a lonely and disappointing third, ahead of fast-finishing Finn Kimi Raikkonen.
With Bottas leading a tight train of five drivers early in the race, Vettel opted for the undercut, pitting for new super softs on Lap 10, with Red Bull's Max Verstappen following suit from fourth place shortly after.
Daniel Ricciardo was third for Red Bull, despite Renault power unit issues halting his programme early, just ahead of Romain Grosjean, who clocked up nearly twice as many for Haas. "Our focus was on advancing our understanding of the tyres and also the rear of the auto so that we can improve our long runs - particularly during the race and on the SuperSoft compound".
"I believe before pit entry that was fine, but here, where he's not going quick, I believe that's why he got the penalty".
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