Hamilton slowed his pace to put Rosberg under pressure in a last-ditch attempt to revive his championship hopes, but Mercedes were more concerned with taking a secure victory.
Despite ordering his driver to speed up over the radio, after the race Lowe refused to call out Hamilton for his tactics.
"I don't want to comment too much on the subject because who knows, we weren't driving the car," Lowe told Sky Sports. "Who knows what the real pace is of a car when you are not driving it."
"It did present some challenges, in end Lewis and Nico were out there racing," he added. "I think it was great to see Sebastian coming through with what turned out to be a very good strategy from Ferrari to get him ahead of the two Red Bulls."
"It was nail-biting stuff for us on the pit wall, those final two laps, would he get through Nico or even Lewis."
Hamilton meanwhile felt his tactics were fair, and couldn't understand Mercedes' decision to impose team orders.
"I don't know why they didn't let us just race," Hamilton said. "There was never a moment where I felt I was going to lose the race. But their thought process was quite clear."
"I don't think I did anything dangerous, I don't think I did anything unfair," he insisted. "We were fighting for the championship, I was in the lead so I control the pace. That is the rules."
Bahrain International Circuit - Winter testing