Both riders were battling for fifth place with three laps to go at the Algarve International Circuit when they made contact on a turn and crashed, with Bagnaia unable to finish the race while Marquez eventually finished 16th, just outside the points.
MotoGP stewards investigated the incident and did not sanction either rider, a decision that was accepted by both six-time champion Marquez and reigning champion Bagnaia.
"I told the stewards it's a racing incident on the very limit. But the stewards must decide what is the limit," Marquez told reporters.
"For me, it was a mistake from Pecco (Bagnaia), but not just the incident because in the end he tried to come back. It was too optimistic and contact can happen... He was suffering a lot, especially with the rear tyres.
"In the end when three, four laps remain, you know you will lose the position. So it's not necessary to come back in that aggressive mode, but he decided this and the consequence to Ducati is zero points."
Bagnaia admitted he was in trouble as he did not have the pace to compete for a podium, but added that the overtake he attempted was not risky.
"When a rider in front of you who you are battling with goes wide, what do you want to do? Overtake him again to take more points. So for me, it wasn't risky," he said.
"I tried to be in front as (much as) possible, but when Pedro (Acosta) arrived, he was too fast. And when Marc arrived, he just tried to overtake, he went wide.
"I tried to close the line. He crossed his line and we collided. It's something that makes me angry, but it's normal. It's a racing incident and we have to move on to the next one."
Bagnaia's crash cost him dearly as he fell from first in the championship to fourth, 23 points behind leader Jorge Martin (26), who won Sunday's race after taking the lead on the opening lap. Marquez is sixth, a further 10 points behind.
The next race weekend is the Grand Prix of the Americas in Austin, Texas on April 12th-14th.
