Nicholson edged out runner-up Tom McDonald, while Jack Trengove, Nathan Jones and Rohan Bail rounded out the top five.
Under the watchful eye of elite performance manager Dave Misson, Melbourne held its first three-km time-trial in early November and its second in December.
Its third and final three-km time-trial for the pre-season was a strong indication on how far the group has improved, according to Misson.
“We had a good group run under 10 mins 20 sec,” he told melbournefc.com.au.
“We’ve had a lot of guys improve significantly from the first time they did it in November until now. Some guys have shaved over a minute off their three-km time.
“More importantly, the team average is down to where we wanted it to be. Essentially, it’s showing that there is good reward for the effort they put in.
“All it’s doing is providing us a base for them to improve their repeat speed and repeat speed efforts, which is what the game’s about.”
Misson said benchmarks and personal bests were commonplace during Friday’s run.
“We were looking at individuals and a couple of significant benchmarks - how many players have we got under 10 minutes? How many under 10 mins 20 sec and how many we’ve got under 10 mins 40 sec. They’re the three benchmarks that we’re looking at,” he said.
“We only had two players [from Friday’s three-km time-trial] who didn’t better their times from last time.
“We had 23 out of 25 who ran PBs (personal bests).”