The rest of the half passed with little in the way of goalmouth action, although Lee Gregory did flash a shot narrowly over the bar with the interval approaching.
However, three minutes into the second half Walton curled a delightful free kick beyond the reach of Stephen Bywater to level the scores.
A few minutes later, Bywater was alert to push Tom Pett's effort away as it looked destined for the far corner.
Walton then showed his dead-ball prowess once more as he sent a second free kick into the back of the net, this time off the frame of the goal.
Jermaine Easter squandered a glorious chance to equalise in the 61st minute, but he did make it 2-2 from the spot just three minutes later after Fred Onyedinma was clumsily pushed over inside the area.
Millwall looked the likelier of the two sides to grab a winner, and John Marquis rattled the crossbar with a strong header, but Stevenage held on.