Messi opened the scoring with a curling shot after superb interplay with Neymar and Kylian Mbappe.
However Benfica earned a draw when Danilo Pereira turned an Enzo Fernandez cross into his own net.
The result means both sides have seven points from three games in Group H.
On this basis, Benfica and PSG both deserve a spot in the round of 16 as they played out a very entertaining encounter where only strong performances by goalkeepers Gianluigi Donnarumma and Odysseas Vlachodimos prevented the scoreline being much larger.
The opener came on 22 minutes and was vintage Messi. A superb team move in from the right side, Messi picked the ball up and combined superbly with fellow forwards Neymar and Mbappe before curling unstoppably into the back of the net.
Benfica are the 40th different opponent the Argentine has scored against in the Champions League, and this was a strike to sit alongside any of Messi’s finest – but it was cancelled out on 41 minutes.
A floated cross from the left wing by Fernandez, after Neymar had sloppily given the ball away, deflected off Danilo and dropped inside the far post for an own goal.
The second half saw PSG apply plenty of pressure, and they hit the bar on 50 minutes when Neymar attempted a spectacular overhead kick following Vlachodimos denying right-back Achraf Hakimi one-on-one.
Vlachodimos made further fine saves from Neymar and Hakimi, while Nicolas Otamendi missed Benfica’s best opportunity when heading wide from six yards.
However both teams had to settle for a point, before they meet again in Paris next week.