The coach, with an eye on Wednesday's Champions League semi-final second leg in Barcelona, rested most of his first-choice defence and midfield despite Inter no longer being favourites for the scudetto having let a nine-point lead slip.
The ploy worked, with Inter going two points clear of AS Roma, who lost 2-1 at home to Sampdoria on Sunday. However, the risk could easily have backfired with just three games left this term.
"It's an important win, we'll see what it means," Kenyan midfielder McDonald Mariga told Sky TV.
"It's a great team with great players so it's hard to get a game here (but) I'm happy," added Mariga after netting his first goal since leaving Parma in January.
Third-bottom Atalanta, who have sparked to life in recent weeks in a late dash to avoid relegation, took the lead on five minutes when striker Simone Tiribocchi slammed the ball in after beating the home team's lax offside trap.
Inter reserve defender Marco Materazzi, 36, was exposed and minutes later the unmarked Tiribocchi headed just wide.
Mourinho screamed on the touchline and his side finally found some fluidity midway through the first half, Argentina striker Diego Milito producing a perfect lob to make it 1-1.
Milito, now on 20 Serie A goals this season, may also have been rested had Mario Balotelli been allowed to play.
TEAM HARMONY
The combustible 19-year-old argued with fans and threw his shirt away after Tuesday's 3-1 first-leg win over Barca but was included in the squad against Atalanta after an apology.
However, club president Massimo Moratti decided late on Friday that Balotelli should not feature for the good of team harmony as media speculation mounts the player will leave.
In the end his absence did not matter with Mariga prodding the ball in on 35 minutes before Cristian Chivu lashed in the third goal in the second half.
Wesley Sneijder went off at half time with a leg problem.
NEWS:Sneijder doubtful for Barca clash
Palermo kept their Champions League hopes alive after an easy 3-1 home win over an injury-crippled AC Milan, who are out of the title race.
Cesare Bovo netted after a corner and Abel Hernandez scored with aplomb in the first half before Clarence Seedorf and Fabrizio Miccoli exchanged second-half strikes to leave third-placed Milan six points above Palermo with three games left.
The defeat will increase media speculation about the future of Milan boss Leonardo after chief executive Adriano Galliani said last week the Brazilian could leave for personal reasons. Reports tip assistant coach Filippo Galli to take over.
