Oleh Blokhin's men pegged the Portuguese champions back twice, Oleg Gusev's header cancelling out Silvestre Varela's fine individual effort within 20 minutes.
Colombian striker Martinez sent the hosts in ahead at the break after good work from countryman James Rodriguez, only for Brown Ideye to level in the 71st minute.
But after Martinez hit his seventh goal of the season, Porto held out to stay top of their group ahead of big-spending French outfit Paris St Germain.
Dynamo Kiev were quickest out of the blocks and Ideye gave Helton an early scare as his corner threatened to sneak in at the far post.
But in the 15th minute, Varela took Lucho Gonzalez's cross under control with one confident touch, striding across the 'D' to flick up the ball and rifle it past Olexandr Shovkovskiy.
Helton coped better than his counterpart five minutes later as he tipped Miguel Veloso's shot round a post, but Dynamo would get their equaliser from the resulting corner.
Veloso swung the ball into the area, Gusev rising above every Porto defender to glance home a header from close range.
A scrappy phase of push-and-run followed, Varela's dangerous header a rare highlight, before Porto edged into the lead once again in the 36th minute.
In a delightful move, Martinez squeezed the ball under Shovkovskiy after fending off Yevhen Khacheridi to make the most of Rodriguez's sumptuous pass.
Martinez threatened to grab his second just after the break but his snapshot sailed over the bar, with Ognjen Vukojevic forced to block Rodriguez's rising effort moments later.
The Estadio do Dragao was subjected to a 20-minute stretch of attritional football but Dynamo made up the required ground to eke out an equaliser.
In the 71st minute, Nigeria international Ideye chested down Andriy Yarmolenko's diagonal pass from deep before rattling the ball beyond Helton.
But Martinez ensured the parity would not last very long with his cool conversion from Gonzalez's slide-rule pass just six minutes later.
Maicon fancied his chances of wrapping up all three points with a swerving free-kick deep into stoppage time, but Porto had already done enough.