He start from 8th place and struggle until he finidh 5th place.
The 26-year-old Spanish rider had surgery in Barcelona in the early hours of Friday before returning to Assen less than 12 hours later.
He took part in the race warm-up on Saturday and was eighth fastest.
"I have decided to race. Just finishing the race would be a small victory for me," said Lorenzo.
"I would like to take at least five points or more - to take less would not be much after suffering a lot.
"At the end of the race we'll see if it was worth it. I'm proud of myself for the effort in these two difficult days after the crash and also of my team for their support."
Lorenzo, who lost control in wet conditions during second free practice on Thursday, had a titanium plate and eight screws inserted into his collarbone.
The Spaniard, who lies seven points behind leader and compatriot Dani Pedrosa in the 2013 standings, will start in 12th place.
"In the first laps of the warm-up I felt a lot of pain, especially when the bike accelerated and I had to hold it strongly," said Lorenzo.
"I thought of either giving up or continuing but luckily I continued and the pain decreased as I did more laps.
"I've grown accustomed to moulding my body to the bike to avoid pain. The problem will be in the race when I have to overtake on the brakes because I can't force the shoulder a lot."
Cal Crutchlow will start the race from pole after becoming the first British MotoGP rider in more than a decade to achieve the feat. Pedrosa will start in fifth.
The last time Lorenzo missed a race was when he relinquished the world title to Australia's Casey Stoner in Phillip Island two years ago.
In November 2009 Lorenzo had an operation to remove a titanium plate - fitted following a crash in the 250cc race at the Circuit de Catalunya in 2005 - from the same collarbone.
