The win gives Marquez a perfect total of 225 points with Pedrosa taking sole possession of second but 77 points back and Italian Valentino Rossi, who finished fourth third in the rankings and 84 adrift.
He is also the youngest rider to win nine races in a row, breaking the 1984 record held previously by the late Englishman Mike Hailwood.
The race, which was threatened by rain caused a farcical start to the proceedings, as a group of some 14 riders got caught trying to change tyres at the last minute and had to wait in the pit-lane until the bikes already on the
grid in dry tyres had gone past.
"It was tough and when I saw (Stefan) Bradl changing tyres at the beginning I thought that was the right choice because there was only one corner that was completely wet so I went in," said the defending champion Marquez, who was one of the riders to get caught out.
"It is marvellous this run I am on, scarcely beleivable. Everyone went in (to change tyres) and my main rivals are Dani (Pedrosa) and Valentino (Rossi) so when I saw them go in, I followed but it worked out ok." continued Marquez
The race began with only nine riders in their allocated qualifying positions as the guessing game to judge the right tyres caused chaos and a mad dash to change to the drying conditions.
Bradl, the 2011 Moto2 world champion, took advantage to lead for the opening stages before Marquez glided past the German with 24 laps to go.
It then came down to a straight battle between Marquez and Pedrosa with Lorenzo well back in third and Italy's Valentino Rossi also cut adrift back in fourth place.
Pedrosa applied what pressure he could on his teammate but Marquez rode with supreme confidence and continued to set the fastest laps of the race as he accelerated further and further into the distance.
"We were comfortable in front, myself and Marc, and we held them off easily," said Pedrosa.
"He had about half a second on me and I couldn't catch him but I had a good race, I'm happy and my team did a really good job," added Pedrosa.
There are nine races to go in the 2014 season with the next round set for Indianapolis on August 10.