McLaren new boy Lando Norris put an impressive lap on his grand prix debut to line up eighth on the grid with Kimi Raikkonen and Sergio Perez rounding off the top ten.
He never let Hamilton back into the race, a striking contrast with 2018.
Bottas went winless last season but said this victory was a definitive performance. We were not battling for the first position, but fourth and fifth.
However, he spent time in Finland working hard in the close season and Bottas says his hard work and a combined team effort paid off this weekend.
Williams appear to have made little progress from past year when they propped up the constructors' championship.
But the German would have hoped for better after qualifying third on Saturday.
But 10 laps to go there was no reason to take risks.
"I don't know what their problem was but I am sure they will come back strongly in the next races, so we have to stay on our toes".
With Mercedes teammate Hamilton also gunning for the fastest lap throughout the race, team boss Toto Wolff has now revealed that the pair went against his pre-race orders.
While investigations into the unexpected performance slump were already ongoing at the track and back at their Italian headquarters, Binotto said it was "too early to have a proper judgement".
The pressure is also mounting on the shoulders of Sebastian Vettel, the team's de facto No. 1 driver and four-time series champion.
He added: "Obviously, the key thing for me was the race start, to get to the lead and then being at the front I could show strong pace and I could pull a gap".
At one point, Vettel even asked his engineer on the radio, "Why are we so slow?".
Vettel added: "In Barcelona we were very happy with the vehicle from day one".
The Brit is chasing the outright second spot in the list of all-time title winners behind Michael Schumacher.
The Finnish driver finished nearly 21 seconds ahead of second placed Lewis Hamilton (Mercedes), while Red Bull's Max Verstappen finished in third place. "I can't say criticism is unfair because everyone can say what they want but maybe they should look in the mirror and think why they do that".
"When he left, after the Christmas party, he said he was exhausted and he needed to recover because it was the most shitty half of the season he has ever had", revealed the Austrian, "and he came back at the end of January and said: "I'm back". Not quite sure what the issue was".