The £85m signing from West Ham met a long punt clear from MK Dons goalkeeper Craig MacGillivray on the volley, guiding it via the post into the top corner from 20 yards to hand Roberto de Zerbi's side a 1-0 win over the League One club.
It was Fernandes' first involvement since his club-record move from West Ham, and the 22-year-old wasted no time making an impression, describing the goal as the finest of his career.
"It was my favourite goal of my career. By a mile," he said. "I need to do this more and more times, to shoot outside of the box, I know that I can do it.
"This just gives me confidence for the rest of the days."
Fernandes lined up alongside fellow big-money arrival Sandro Tonali in a double pivot, with the £100m signing from Newcastle also making his first appearance for the club. Together, the pair - signed for a combined £185m - dominated the midfield exchanges before both were withdrawn at half-time as De Zerbi rotated his side.
Former Spurs defender Sebastian Bassong, working for the club's media channels, was among those to draw favourable comparisons for Fernandes' strike, likening it to celebrated volleys from Gareth Bale and Zinedine Zidane.
"What I'm impressed about is the balance, the quality, the connection, the fact that he's looking at the ball - he doesn't lose sight of the ball," Bassong said.
"He's such a gifted player."
Elsewhere, goalkeeper Martin Dubravka impressed with a sharp stop on his first outing since arriving on a free transfer from Burnley in June. Introduced at the break for Antonin Kinsky, Dubravka reacted well to push a header from six yards over the bar, in what was otherwise a quiet second half for both goalkeepers.
The result offers early encouragement for a Spurs side that only secured their Premier League survival on the final day of last season, before a dramatic upturn in transfer activity under De Zerbi. That summer overhaul has already brought in Andy Robertson, Marcos Senesi, Jan Paul van Hecke and Dubravka alongside the two big-money midfield arrivals, with Fernandes joining after a breakout campaign at West Ham following his move from Southampton last year.
A tougher test awaits on their pre-season tour, with the club flying to New Zealand on Thursday ahead of a friendly against A-League side Auckland at Eden Park on Sunday.