The pair collided while part of a four-bike lead battle with eventual winner Andrea Iannone and Thomas Luthi. Marquez was recovering from a moment going into Turn 10 on lap 21 of the 23-lap race when Espargaro attempted to go down his inside. Firm contact was made as Marquez tried to regain the racing line, causing Espargaro to crash heavily. The Pons rider was unhurt, while Marquez went on to finish third behind Iannone and Luthi.
Race direction decided Marquez was at fault and gave him a one-minute penalty, dropping him to 23rd in the race results, and from second to fourth in the championship - 18 points behind leader Luthi. Marquez's Monlau team has appealed against the decision.
Earlier in the year Marquez had received a reprimand from the officials but no penalty for a controversial incident with Luthi as they battled for the lead of the Qatar round.
Both Stoner and Rossi felt that Marquez had been treated unfairly.
"Can't believe they gave Marc Marquez a one-minute penalty!" Stoner wrote on his Twitter feed. "Another reason why this championship needs some sorting out! I've seen much worse."
Rossi said that while Marquez had been at fault in Qatar, in this instance he reckoned the blame lay with Espargaro.
"For me, Marc did one bad manoeuvre at Qatar on the last lap with Luthi, but for me today was not a mistake from Marquez," said Rossi. "He was in front and it was impossible to see Espargaro.
"It is more a mistake from Espargaro to try in one place with not enough space for two bikes."