Rooney, captain in the absence of the suspended Steven Gerrard and the injured Frank Lampard, marked the occasion by becoming his country's fifth highest scorer of all time on 31 goals.
Alex Oxlade-Chamberlain also notched his first international goal as Roy Hodgson's side found the net three times in the last 20 minutes in front of an 84,000 crowd at Wembley as San Marino wilted after frustrating England for most of the match.
After being treated for five minutes on the field, the Arsenal winger was taken to hospital for a chest scan and replaced by Tottenham Hotspur's Aaron Lennon.
Hodgson later called Simoncini's challenge "reckless". Looking at the game overall he said he was pleased with England's display even though it took them 35 minutes to make the breakthrough.
"There could have been a lot more goals but certainly there was a lot of goalmouth action and there was a lot of quality passing. They were two positive aspects of the evening," Hodgson told reporters.
"The third positive aspect was in Moldova where they drew 0-0 with Ukraine. Most people expected Ukraine to win there and that of course is good news for us."
Hodgson's team travel to Poland on Tuesday for a much stiffer test than the one bottom of the table San Marino provided on Friday.
They went in front a minute later with Rooney's penalty and Welbeck quickly made it 2-0 with a clever close-range flick from a pass by Lennon.
England were expected to chalk up a landslide win over the visitors who are joint bottom of FIFA's world rankings with only one victory in 115 matches and no away goals in 23 games dating back to August 2003.
