Kevin De Bruyne was also on target from the penalty spot as City recorded back-to-back league wins for the first time this season to move into the top four.
Sterling had not scored in the league for nearly two months and been left out by Guardiola in recent weeks.
But the England international looked more like his old self to provide some much-needed penetration in behind for a City side that has struggled to score goals this season.
Sterling should have opened the scoring inside three minutes when he fired too close to Alphonse Areola after Riyad Mahrez's pass opened up the Fulham defence.
Less than two minutes later, Sterling got a second chance from another sumptuous De Bruyne assist and this time made no mistake on his favoured right foot for a first goal in seven games.
Sterling then helped create the second as he turned Joachim Andersen inside the box and went down under the faintest contact from the Danish defender for a penalty.
De Bruyne had missed his last spot-kick against Liverpool, but confidently strode forward to send Areola the wrong way and end the game as contest just 26 minutes in.
Another flying save from Areola then denied Sterling a spectacular second with an acrobatic volley.
John Stones is enjoying a renaissance at the heart of Guardiola's defence as he was again preferred to Aymeric Laporte alongside Ruben Dias.
However, it was a mix-up between Stones and Ederson that came closest to providing Fulham a lifeline as the goalkeeper came rushing off his line to clear as Stones played the ball back towards his own goal and was relieved to see it roll wide for a corner.
After scoring just 10 goals in their first eight league games of the season, City clicked into gear last weekend in a 5-0 thrashing of Burnley.
Had De Bruyne been more clinical, the hosts could have had another handful.
The Belgian turned Gabriel Jesus's pass onto the crossbar then could not beat Areola when one-on-one after a brilliant through ball from Mahrez set him clear.
Mahrez was the creator again with a well-worked corner for De Bruyne's next effort which flew well over the bar.
But two goals were more than enough as City recorded a fourth consecutive clean sheet.
At the other end of the table, Fulham remain just a point clear of the relegation zone in 17th.