Two first half goals from Lautaro Martinez were enough to hold off the second half fight of the relegation candidates.
Earlier in the day, champions Juventus were held to a 2-2 draw at home to Sassuolo, which allowed Inter to move onto 37 points, one point better than Maurizio Sarri’s men, who remain unbeaten.
Conte, who has won league titles in Italy and England, has played down Inter’s title chances despite their status as the new leaders, but is delighted by how far his charges have improved.
“We've been working since day one to make an impact and annoy the other teams," Conte told Sky Sport Italia.
"Being back on top of the table after 14 rounds makes us proud, because we know the journey we've been through to get here.
"At the same time, it should give us positive enthusiasm, push us to do even better and control the game without suffering to the end the way we did, because in those circumstances a cross or deflected shot can change everything.
"We were determined and knew Juventus had dropped points, so we were prepared to make the most of the situation.
"We deserved to beat SPAL and it's important to remember we are focused on our own growth process, which is in full swing, so we're not trying to compare ourselves with others."