In the end, Bottas took the second place while Sebastian Vettel of Ferrari emerged as the eventual victor of the race with an official time of 1:32:01.940.
Hamilton's teammate Valtteri Bottas will also take on a new gearbox, but, under the sport's rules, avoids a penalty as he is permitted a free change after his qualifying crash in Australia.
Will Sebastian Vettel be victorious from pole at the Bahrain GP?
The next race is in less than a weeks' time at the Shanghai International Circuit, China, and Hamilton is keen to get back to winning ways on circuit where he has won five times in the past.
Raikkonen and Vettel finished half-a-second clear of their Mercedes rivals in practice.
"My thoughts are already on the world championship", Hamilton told Sky Sports F1 after the race in Bahrain. Mercedes F1 boss Toto Wolff defended his driver though by reasoning out that it was only a racing incident. "Or I've got to catch him while the tyres are still good and close the gap to the best of my ability, because they're doing a one-stop".
"We got a bit squeezed but from the middle to the end of the corner I was ahead, I then felt a nudge from behind and could feel the puncture and therefore knew the race was likely over".
Hamilton, meanwhile, has hit back at Red Bull Racing driver Verstappen, after the pair collided early in the race.
With Red Bull suffering a double retirement after Daniel Ricciardo lasted only two laps, sister team Toro Rosso capitalised, with Pierre Gasly finishing a surprise fourth.
Then, the Briton was involved in an early collision with Ferrari's Max Verstappen at the early part of the race.
"Calling him a "****head" in the cool-down room as he watched highlights of the grand prix, Hamilton later added: "There needs to be a certain respect between drivers.
"I was driving in no-man's land for a while, that's something we need to work on", Hamilton said.
"He [Verstappen] should have finished a decent race, because he's good enough. It was a silly manoeuvre from him because he didn't finish the race".